Descriptor: "génomique fonctionnelle" / Topic: 03 medical and health sciences - Searchworks@Jio Institute Digital Library Search Results

Your search keyword '"génomique fonctionnelle"' showing total 38 results

Start Over Descriptor "génomique fonctionnelle" Topic 03 medical and health sciences

38 results on '"génomique fonctionnelle"'

1. ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity

Author: Christelle Hennequet-Antier, Amélie Juanchich, Aurélien Brionne, Brionne, Aurélien, Juanchich, Amélie, Hennequet-Antier, Christelle, Biologie des Oiseaux et Aviculture (BOA), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), and Institut National de la Recherche Agronomique (INRA)-Université de Tours
Subjects: Computer science, [SDV]Life Sciences [q-bio], Annotation, génomique fonctionnelle, Short Report, lcsh:Analysis, Ontology (information science), lcsh:Computer applications to medicine. Medical informatics, Biochemistry, Bioconductor, Gene ontology, Functional genomics, Visualization, Cluster analysis, Semantic similarity, Enrichment test, 03 medical and health sciences, Genetics, Ensembl, [INFO]Computer Science [cs], analyse par cluster, fonction biologique, Molecular Biology, ontologie, 030304 developmental biology, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, relation semantique, Information retrieval, gène, 030302 biochemistry & molecular biology, lcsh:QA299.6-433, Computer Science Applications, Computational Mathematics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Computational Theory and Mathematics, lcsh:R858-859.7, UniProt
Abstract: The main objective of ViSEAGO package is to carry out a data mining of biological functions and establish links between genes involved in the study. We developed ViSEAGO in R to facilitate functional Gene Ontology (GO) analysis of complex experimental design with multiple comparisons of interest. It allows to study large-scale datasets together and visualize GO profiles to capture biological knowledge. The acronym stands for three major concepts of the analysis: Visualization, Semantic similarity and Enrichment Analysis of Gene Ontology. It provides access to the last current GO annotations, which are retrieved from one of NCBI EntrezGene, Ensembl or Uniprot databases for several species. Using available R packages and novel developments, ViSEAGO extends classical functional GO analysis to focus on functional coherence by aggregating closely related biological themes while studying multiple datasets at once. It provides both a synthetic and detailed view using interactive functionalities respecting the GO graph structure and ensuring functional coherence supplied by semantic similarity. ViSEAGO has been successfully applied on several datasets from different species with a variety of biological questions. Results can be easily shared between bioinformaticians and biologists, enhancing reporting capabilities while maintaining reproducibility. ViSEAGO is publicly available on https://bioconductor.org/packages/ViSEAGO .
Published: 2019
Full Text: View/download PDF

2. An evolutionary approach to recover genes predominantly expressed in the testes of the zebrafish, chicken and mouse

Author: Philippe Monget, Aurore Thélie, Floriane Picolo, Sébastien Elis, Marina Govoroun, Sophie Fouchécourt, Charlotte Lécureuil, Pascal Papillier, Jean-Jacques Lareyre, Mégane Bregeon, Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS), Institut de recherche sur la biologie de l'insecte UMR7261 (IRBI), Université de Tours-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Recherche Agronomique (INRA), FertilMale, Conseil Régional du Centre-Val de Loire (), 677353 (IMAGE), European Union's Horizon 2020 Research and Innovation Programme, CRB Anim, Investissements d'avenir, PHASE, institut national de la recherche agronomique, Centre National de la Recherche Scientifique (CNRS)-Université de Tours-Institut Français du Cheval et de l'Equitation [Saumur]-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur] (IFCE)-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), and Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Male, 0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], génomique fonctionnelle, poisson zèbre, souris, 01 natural sciences, Genome, poisson, cyprinidae, flies, mouche, Zebrafish, Phylogeny, Genetics, biology, conservation, Vertebrate, mus musculus, Phenotype, medicine.anatomical_structure, danio rerio, testicule, Drosophila melanogaster, danio devario, Germ cell, Research Article, expression des gènes, animal structures, mice, Evolution, animal fertility, In silico, chicken, gene evolution, testis, spermatogenesis, spermatogenèse, poulet, analyse phylogénétique, 010603 evolutionary biology, drosophila melanogaster, Evolution, Molecular, reproduction, 03 medical and health sciences, biology.animal, QH359-425, medicine, Animals, gène orthologue, Gene, Ecology, Evolution, Behavior and Systematics, fish, fungi, fertilité animale, biology.organism_classification, vertébré, 030104 developmental biology, évolution génétique des populations, fonction des gènes, vertebrates, Chickens
Abstract: Background Previously, we have demonstrated that genes involved in ovarian function are highly conserved throughout evolution. In this study, we aimed to document the conservation of genes involved in spermatogenesis from flies to vertebrates and their expression profiles in vertebrates. Results We retrieved 379 Drosophila melanogaster genes that are functionally involved in male reproduction according to their mutant phenotypes and listed their vertebrate orthologs. 83% of the fly genes have at least one vertebrate ortholog for a total of 625 mouse orthologs. This conservation percentage is almost twice as high as the 42% rate for the whole fly genome and is similar to that previously found for genes preferentially expressed in ovaries. Of the 625 mouse orthologs, we selected 68 mouse genes of interest, 42 of which exhibited a predominant relative expression in testes and 26 were their paralogs. These 68 mouse genes exhibited 144 and 60 orthologs in chicken and zebrafish, respectively, gathered in 28 groups of paralogs. Almost two thirds of the chicken orthologs and half of the zebrafish orthologs exhibited a relative expression ≥50% in testis. Finally, our focus on functional in silico data demonstrated that most of these genes were involved in the germ cell process, primarily in structure elaboration/maintenance and in acid nucleic metabolism. Conclusion Our work confirms that the genes involved in germ cell development are highly conserved across evolution in vertebrates and invertebrates and display a high rate of conservation of preferential testicular expression among vertebrates. Among the genes highlighted in this study, three mouse genes (Lrrc46, Pabpc6 and Pkd2l1) have not previously been described in the testes, neither their zebrafish nor chicken orthologs. The phylogenetic approach developed in this study finally allows considering new testicular genes for further fundamental studies in vertebrates, including model species (mouse and zebrafish). Electronic supplementary material The online version of this article (10.1186/s12862-019-1462-8) contains supplementary material, which is available to authorized users.
Published: 2019
Full Text: View/download PDF

3. The chromosome-level genome assembly of european grayling reveals aspects of a unique genome evolution process within salmonids

Author: Savilammi, Tiina, Primmer, Craig R., Varadharajan, Srinidhi, Guyomard, Rene, Guiguen, Yann, Sandve, Simen Rød, Asbjørn Vøllestad, L., Vøllestad, Leif Asbjørn, Papakostas, Spiros, Lien, Sigbjørn, Department of Biology, University of Memphis, Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsinki Institute of Life Science (HiLIFE), University of Helsinki-University of Helsinki-Helsinki Institute of Life Science (HiLIFE), University of Helsinki-University of Helsinki, University of Helsinki, Department of Biosciences, University of Kent [Canterbury], Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Centre for Integrative Genetics (CIGENE), ANR Blanc SVSE 7 - 2011 (Project SDS), This work was supported by the Academy of Finland (project numbers 287342 and 302873). We thank the Finnish Centre for Scientific Computing for providing computational resources. SV and LAV are supported by Center for Computational Inference in Evolutionary Life Science (CELS) and the Department of Biosciences, University of Oslo. YG and RG contributions were supported by the Agence Nationale de la Recherche (ANR Blanc SVSE 7 2011, project SDS)., ANR-15-CE37-0004,SmellBrain,Dissection fonctionnelle des circuits codant pour la récompense dans le système olfactif(2015), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Recherche Agronomique (INRA), Helsinki Institute of Sustainability Science (HELSUS), Evolution, Conservation, and Genomics, Institute of Biotechnology, and Organismal and Evolutionary Biology Research Programme
Subjects: 0106 biological sciences, Male, Genetic Linkage, [SDV]Life Sciences [q-bio], génomique fonctionnelle, chromosome evolution, Retrotransposon, QH426-470, 01 natural sciences, Genome, ANNOTATION, poisson, salmonids, DRIVERS, chromosome, ombre commun, Salmo, Genetics (clinical), salmonidae, 0303 health sciences, biology, REARRANGEMENTS, 1184 Genetics, developmental biology, physiology, Chromosome Mapping, karyotype evolution, karyotyping of the cells, Genomics, Thymallus, gène sdY, retrotransposons, ALIGNMENT, séquençage du génome, caryotype, évolution du génome, chromosomal structure, Female, rétrotransposon, Genome evolution, DATABASE, Centromere, Salmo salar, genomic rearrangements, 010603 evolutionary biology, Chromosomes, CLASSIFICATION, thymallus thymallus, Evolution, Molecular, reproduction, 03 medical and health sciences, Genetics, Animals, 14. Life underwater, Molecular Biology, 030304 developmental biology, Synteny, Repetitive Sequences, Nucleic Acid, fish, IDENTIFICATION, Chromosome, Computational Biology, biology.organism_classification, GENE, Genome Report, European grayling, Evolutionary biology, ORIGINS, structure chromosome, évolution chromosomique, SYSTEM
Abstract: Supplemental material available at Figshare: https://doi.org/10.25387/g3.7728512; Salmonids represent an intriguing taxonomical group for investigating genome evolution in vertebrates due to their relatively recent last common whole genome duplication event, which occurred between 80 and 100 million years ago. Here, we report on the chromosome-level genome assembly of European grayling (Thymallus thymallus), which represents one of the earliest diverged salmonid subfamilies. To achieve this, we first generated relatively long genomic scaffolds by using a previously published draft genome assembly along with long-read sequencing data and a linkage map. We then merged those scaffolds by applying synteny evidence from the Atlantic salmon (Salmo salar) genome. Comparisons of the European grayling genome assembly to the genomes of Atlantic salmon and Northern pike (Esox lucius), the latter used as a nonduplicated outgroup, detailed aspects of the characteristic chromosome evolution process that has taken place in European grayling. While Atlantic salmon and other salmonid genomes are portrayed by the typical occurrence of numerous chromosomal fusions, European grayling chromosomes were confirmed to be fusion-free and were characterized by a relatively large proportion of paracentric and pericentric inversions. We further reported on transposable elements specific to either the European grayling or Atlantic salmon genome, on the male-specific sdY gene in the European grayling chromosome 11A, and on regions under residual tetrasomy in the homeologous European grayling chromosome pairs 9A-9B and 25A-25B. The same chromosome pairs have been observed under residual tetrasomy in Atlantic salmon and in other salmonids, suggesting that this feature has been conserved since the subfamily split.
Published: 2019
Full Text: View/download PDF

4. Towards a tailored indoor horticulture: a functional genomics guided phenotypic approach

Author: Xinyun Liu, Huiting An, Nuo Xu, Shihui Huang, Xutong Pan, Aloysius Wong, Claudius Marondedze, Cindy Wong, Xuechen Tian, Xuan Zhou, Physiologie cellulaire et végétale (LPCV), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Wenzhou Medical University, Partenaires INRAE, University of Toronto, Student-partnering-with-Faculty (SpF) program of Wenzhou-Kean University, Zhejiang China WKU201718009, Office of Research and Sponsored Programs of Wenzhou-Kean University, and Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG)
Subjects: 0106 biological sciences, 0301 basic medicine, Plant growth, Botanics, caractère phénotypique, Mini Review, génomique fonctionnelle, Plant Science, Biology, 01 natural sciences, Biochemistry, 03 medical and health sciences, Electric light, lcsh:Botany, Genetics, Plant traits, lcsh:QH301-705.5, 2. Zero hunger, business.industry, fungi, horticulture, food and beverages, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Sustainable food production, lcsh:QK1-989, Light quality, Botanique, Horticulture, 030104 developmental biology, lcsh:Biology (General), Agriculture, Plant species, business, Functional genomics, 010606 plant biology & botany, Biotechnology
Abstract: As indoor horticulture gathers momentum, electric (also termed artificial) lighting systems with the ability to generate specific and tunable wavelengths have been developed and applied. While the effects of light quality on plant growth and development have been studied, authoritative and reliable sets of light formulae tailored for the cultivation of economically important plants and plant traits are lacking as light qualities employed across laboratories are inconsistent. This is due, at least in part, to the lack of molecular data for plants examined under electric lights in indoor environments. It has hampered progress in the field of indoor horticulture, in particular, the transition from small-scale indoor farming to commercial plant factories. Here, we review the effects of light quality on model and crop plants studied from a physiological, physical and biochemical perspective, and explain how functional genomics can be employed in tandem to generate a wealth of molecular data specific for plants cultivated under indoor lighting. We also review the current state of lighting technologies in indoor horticulture specifically discussing how recent narrow-bandwidth lighting technologies can be tailored to cultivate economically valuable plant species and traits. Knowledge gained from a complementary phenotypic and functional genomics approach can be harvested not only for economical gains but also for sustainable food production. We believe that this review serves as a platform that guides future light-related plant research., Indoor horticulture: Lighting the way to sustainability Tailored multidisciplinary approaches to hone sustainable indoor horticulture could significantly improve plant yields and crop quality. Advances in artificial lighting systems could transform commercial-scale indoor horticulture, but the current technology is limited by a lack of molecular data for plants grown under such lighting schemes. Aloysius Wong at Wenzhou-Kean University in Wenzhou, China, and co-workers reviewed research into the effects of light quality and differing wavelengths on plant growth. The team advocate the use of plant type-specific and functional genomics studies to examine light-determined molecular traits and associated gene expression. These could be used to build an extensive catalog of light qualities that enhance indoor crop yields and quality. Combining LED lights of different colors and wavelengths shows promise, and the researchers highlight the potential of tunable narrow wavelength lights, such as lasers.
Published: 2018
Full Text: View/download PDF

5. Combined QTL and Selective Sweep Mappings with Coding SNP Annotation andcis-eQTL Analysis RevealedPARK2andJAG2as New Candidate Genes for Adiposity Regulation

Author: Morgane Boutin, M. J. Duclos, Colette Désert, Elisabeth Le Bihan-Duval, Diane Esquerre, Yuna Blum, Sandrine Lagarrigue, Frédérique Pitel, Hervé Guillou, Pierre-François Roux, Etienne Mouisel, Brian W. Parks, Olivier Demeure, Sophie Leroux, Christophe Klopp, Anis Djari, Bertrand Servin, Aldons J. Lusis, Simon Boitard, Alexandra Montagner, Frédéric Lecerf, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Université européenne de Bretagne - European University of Brittany (UEB), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Department of Medecine/Division of Cardiology, University of California [Los Angeles] (UCLA), University of California-University of California, ToxAlim (ToxAlim), Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), SIGENAE, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Recherches Avicoles (URA), Department of Human Genetics, Toxicologie Intégrative & Métabolisme (ToxAlim-TIM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] ( PEGASE ), Institut National de la Recherche Agronomique ( INRA ) -AGROCAMPUS OUEST, Université européenne de Bretagne ( UEB ), Biologie Intégrative des Populations, École pratique des hautes études ( EPHE ) -Centre National de la Recherche Scientifique ( CNRS ), Génétique Animale et Biologie Intégrative ( GABI ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, University of California at Los Angeles [Los Angeles] ( UCLA ), Toxicologie Alimentaire ( UTA ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, UMR 1048 I2MC, Institut National de la Santé et de la Recherche Médicale, Unité de Biométrie et Intelligence Artificielle ( UBIA ), Institut National de la Recherche Agronomique ( INRA ), GenPhySE - UMR 1388 ( Génétique Physiologie et Systèmes d'Elevage ), Institut National de la Recherche Agronomique ( INRA ) -École nationale supérieure agronomique de Toulouse [ENSAT]-ENVT, GENOTOUL, Recherches Avicoles ( SRA ), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), Toxicologie Alimentaire (UTA), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Recherches Avicoles (SRA), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), University of California (UC)-University of California (UC), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Ecole d'Ingénieurs de Purpan (INP - PURPAN), Université de Toulouse (UT)-Université de Toulouse (UT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3)
Subjects: Candidate gene, QTL, [SDV]Life Sciences [q-bio], génomique fonctionnelle, métabolisme des lipides, Mice, selective sweeps, 0302 clinical medicine, Family-based QTL mapping, régulation, Genetics (clinical), Genetics, adiposity, 0303 health sciences, Genome, Chromosome Mapping, High-Throughput Nucleotide Sequencing, adiposité, cis-eQTLs, divergent lines, gène candidat, Jagged-2 Protein, JAG2, Adipose Tissue, White, Ubiquitin-Protein Ligases, Quantitative Trait Loci, poulet, Context (language use), annotation génomique, Myosins, Investigations, Quantitative trait locus, Biology, Polymorphism, Single Nucleotide, Cell Line, 03 medical and health sciences, Gene mapping, séquençage à haut débit, Animals, Molecular Biology, Alleles, 030304 developmental biology, [ SDV ] Life Sciences [q-bio], Membrane Proteins, Molecular Sequence Annotation, Sequence Analysis, DNA, PARK2, détection de qtl, SNP annotation, Expression quantitative trait loci, Selective sweep, Chickens, 030217 neurology & neurosurgery
Abstract: Very few causal genes have been identified by quantitative trait loci (QTL) mapping because of the large size of QTL, and most of them were identified thanks to functional links already known with the targeted phenotype. Here, we propose to combine selection signature detection, coding SNP annotation, and cis-expression QTL analyses to identify potential causal genes underlying QTL identified in divergent line designs. As a model, we chose experimental chicken lines divergently selected for only one trait, the abdominal fat weight, in which several QTL were previously mapped. Using new haplotype-based statistics exploiting the very high SNP density generated through whole-genome resequencing, we found 129 significant selective sweeps. Most of the QTL colocalized with at least one sweep, which markedly narrowed candidate region size. Some of those sweeps contained only one gene, therefore making them strong positional causal candidates with no presupposed function. We then focused on two of these QTL/sweeps. The absence of nonsynonymous SNPs in their coding regions strongly suggests the existence of causal mutations acting in cis on their expression, confirmed by cis-eQTL identification using either allele-specific expression or genetic mapping analyses. Additional expression analyses of those two genes in the chicken and mice contrasted for adiposity reinforces their link with this phenotype. This study shows for the first time the interest of combining selective sweeps mapping, coding SNP annotation and cis-eQTL analyses for identifying causative genes for a complex trait, in the context of divergent lines selected for this specific trait. Moreover, it highlights two genes, JAG2 and PARK2, as new potential negative and positive key regulators of adiposity in chicken and mice.
Published: 2015
Full Text: View/download PDF

6. Long noncoding RNA repertoire in chicken liver and adipose tissue

Author: Sylvain Foissac, Morgane Boutin, Valentin Wucher, Frédéric Jehl, Colette Désert, Elisabetta Giuffra, Diane Esquerre, Frédéric Lecerf, Sandrine Lagarrigue, Christophe Klopp, Kévin Muret, Thomas Derrien, Sarah Djebali, Fabrice Legeai, Hervé Acloque, BMC, BMC, Adapting the feed, the animal and the feeding techniques to improve the efficiency and sustainability of monogastric livestock production systems - Feed-a-Gene - - H20202015-03-01 - 2020-02-29 - 633531 - VALID, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Institut National de la Recherche Agronomique (INRA), Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, IN-1275570, INRA, European Project: 633531,H2020,H2020-SFS-2014-2,Feed-a-Gene(2015), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), and AgroParisTech-Institut National de la Recherche Agronomique (INRA)
Subjects: 0301 basic medicine, Genotype, [SDV]Life Sciences [q-bio], Quantitative Trait Loci, poulet, génomique fonctionnelle, tissu adipeux, Adipose tissue, Biology, Genome, Evolution, Molecular, Transcriptome, Open Reading Frames, analyse de génome, 03 medical and health sciences, Genetics, Animals, Humans, RNA, Antisense, Genetics(clinical), RNA, Messenger, Gene, Conserved Sequence, Ecology, Evolution, Behavior and Systematics, Synteny, 030102 biochemistry & molecular biology, Gene Expression Profiling, General Medicine, Lipid Metabolism, foie, Phenotype, Long non-coding RNA, [SDV] Life Sciences [q-bio], Gene expression profiling, 030104 developmental biology, Adipose Tissue, Gene Expression Regulation, Liver, Organ Specificity, RNA, Long Noncoding, Animal Science and Zoology, Chickens, annotation fonctionnelle, Research Article
Abstract: Background Improving functional annotation of the chicken genome is a key challenge in bridging the gap between genotype and phenotype. Among all transcribed regions, long noncoding RNAs (lncRNAs) are a major component of the transcriptome and its regulation, and whole-transcriptome sequencing (RNA-Seq) has greatly improved their identification and characterization. We performed an extensive profiling of the lncRNA transcriptome in the chicken liver and adipose tissue by RNA-Seq. We focused on these two tissues because of their importance in various economical traits for which energy storage and mobilization play key roles and also because of their high cell homogeneity. To predict lncRNAs, we used a recently developed tool called FEELnc, which also classifies them with respect to their distance and strand orientation to the closest protein-coding genes. Moreover, to confidently identify the genes/transcripts expressed in each tissue (a complex task for weakly expressed molecules such as lncRNAs), we probed a particularly large number of biological replicates (16 per tissue) compared to common multi-tissue studies with a larger set of tissues but less sampling. Results We predicted 2193 lncRNA genes, among which 1670 were robustly expressed across replicates in the liver and/or adipose tissue and which were classified into 1493 intergenic and 177 intragenic lncRNAs located between and within protein-coding genes, respectively. We observed similar structural features between chickens and mammals, with strong synteny conservation but without sequence conservation. As previously reported, we confirm that lncRNAs have a lower and more tissue-specific expression than mRNAs. Finally, we showed that adjacent lncRNA-mRNA genes in divergent orientation have a higher co-expression level when separated by less than 1 kb compared to more distant divergent pairs. Among these, we highlighted for the first time a novel lncRNA candidate involved in lipid metabolism, lnc_DHCR24, which is highly correlated with the DHCR24 gene that encodes a key enzyme of cholesterol biosynthesis. Conclusions We provide a comprehensive lncRNA repertoire in the chicken liver and adipose tissue, which shows interesting patterns of co-expression between mRNAs and lncRNAs. It contributes to improving the structural and functional annotation of the chicken genome and provides a basis for further studies on energy storage and mobilization traits in the chicken. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0275-0) contains supplementary material, which is available to authorized users.
Published: 2017
Full Text: View/download PDF

7. Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture

Author: James W. Kijas, William S. Davidson, Steinar Bergseth, Patricia Iturra, Jon Olav Vik, Rachael J. Ritchie, Louis Bernatchez, Yniv Palti, Anna Wargelius, José M. Yáñez, Ross D. Houston, Craig R. Primmer, Matthew L. Rise, Kerry A. Naish, Alejandro Maass, Kristinn Olafsson, Tom Goldammer, Alfredo Tello, Patricia M. Schulte, Philip McGinnity, Martin Montecino, Sigbjørn Lien, Barbara F. Nowak, Krista M. Nichols, Ben F. Koop, Caird E. Rexroad, Yann Guiguen, Samuel A.M. Martin, Cristian Gallardo-Escárate, Stig W. Omholt, Graham Plastow, Simen Rød Sandve, Rodrigo Vidal, Daniel J. Macqueen, Institute of Biological and Environmental Sciences, (SFIRC), Department of Biology, Northern Arizona University [Flagstaff], The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Institute for Marine and Antarctic Studies [Horbat] (IMAS), University of Tasmania [Hobart, Australia] (UTAS), Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval [Québec] (ULaval), The Research Council of Norway, Department of Molecular Biology and Biochemistry, University of California [Irvine] (UCI), University of California-University of California, Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research, Department of Oceanography, Universidad de Concepción [Chile], Institute for Genome Biology, Fish Genetics Unit, Leibniz Institute for Farm Animal Biology (FBN), Laboratoire de Physiologie et Génomique des Poissons (LPGP), Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Human Genetics Program ICBM Faculty of Medicine, University of Chile, CSIRO, Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences (NMBU), Center for Mathematical Modelling - Centro de Modelamiento Matematico [Santiago] (CMM), Universidad de Chile = University of Chile [Santiago] (UCHILE)-Centre National de la Recherche Scientifique (CNRS), Center for Genome Regulation, FONDAP 15090007, School of Biological, Earth and Environmental Sciences [Sydney] (BEES), University of New South Wales [Sydney] (UNSW), Center for Biomedical Research, Universidad Andrés Bello [Santiago] (UNAB), FONDAP Center for Genome Regulation, Faculty of Biological Sciences and Faculty of Medicine, School of Aquatic and Fishery Sciences, University of Washington [Seattle], Conservation Biology Division [Seattle], Northwest Fisheries Science Center (NWFSC), NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA)-NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA), Norwegian University of Science and Technology [Trondheim] (NTNU), Norwegian University of Science and Technology (NTNU), National Center for Cool and Cold Water Aquaculture, ARS-USDA, USDA-ARS : Agricultural Research Service, Department of Agricultural, Food, and Nutritional Science, University of Alberta, Office of National Programs, Department of Ocean Sciences, Memorial University of Newfoundland [St. John's], Genome British Columbia, Department of Zoology, Auburn University (AU), INTESAL de SalmonChile, Instituto Tecnológico del Salmón S.A., Laboratory of Molecular Ecology, Genomics, and Evolutionary Studies, Department of Biology, University of Santiago, Norwegian Institute of Marine Research, Faculty of Veterinary and Animal Sciences, Universidad de Chile = University of Chile [Santiago] (UCHILE), Aquainnovo, Supported by the International Cooperation to Sequence the Atlantic Salmon Genome (ICSASG), funded by: The Research Council of Norway (RCN), The Norwegian Seafood Research Fund (FHF), Genome British Columbia (GBC, Canada), The Chilean Economic Development Agency (CORFO) and the Innova Chile Committee (InnovaChile). FAASG has also received support from the Biotechnology and Biological Sciences Research Council (UK) (ref: BB/P02582X/1). Initial FAASG pilot studies (currently in process) are being funded by the ICSASG and the U.S. Department of Agriculture (USDA), through NIFA National Research Support Project 8., University of Tasmania (UTAS), Université Laval, Universidad de Concepción, Leibniz Institute for Farm Animal Biology, Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Recherche Agronomique (INRA), University of Chile [Santiago]-Centre National de la Recherche Scientifique (CNRS), Matis Ltd, National Center for Cool and Cold Water Aquaculture, University of Chile [Santiago], and Supported by the International Cooperation to Sequence the Atlantic Salmon Genome (ICSASG), funded by: The Research Council of Norway (RCN), The Norwegian Seafood Research Fund (FHF), Genome British Columbia (GBC, Canada)), The Chilean Economic Development Agency (CORFO) and the Innova Chile Committee (InnovaChile). FAASG has also received support from the Biotechnology and Biological Sciences Research Council (UK) (ref: BB/P02582X/1). Initial FAASG pilot studies (currently in process) are being funded by the ICSASG and the U.S. Department of Agriculture (USDA), through NIFA National Research Support Project 8.
Subjects: 0106 biological sciences, 0301 basic medicine, biologie comparative, Internationality, [SDV]Life Sciences [q-bio], Resistance, génomique fonctionnelle, Aquaculture, 01 natural sciences, Genome, genomic selection, Whole genome duplication, poisson, salmonids, Applied research, évolution génomique des poissons, duplication des génomes, Phylogeny, Genetics, DNA methylation, Populations, Functional annotation, Genomics, Salar, ChIP-seq, phénotype, Rainbow trout, Molecular Sequence Annotation, séquençage du génome, Editorial, Phenotype, Phenotyping, aquaculture, comparative biology, data sharing, evolution, functional annotation, genome biology, phenotyping, standardized data and metadata, salmonid fish, whole genome duplication, Identification (biology), annotation fonctionnelle, Salmonidae, Biotechnology, expression des gènes, Atlantic salmon, Genome evolution, Conservation of Natural Resources, lcsh:QH426-470, Evolution, lcsh:Biotechnology, Comparative biology, Biology, Insights, 010603 evolutionary biology, production aquacole, reproduction, Evolution, Molecular, 03 medical and health sciences, analyse de génome, Standardized data and metadata, lcsh:TP248.13-248.65, Animals, 14. Life underwater, sélection génomique, conservation des espèces, fish, Oncorhynchus tshawytscha, lcsh:Genetics, 030104 developmental biology, Genome biology, Evolutionary biology, variation phénotypique, Genome Biology, Standardized data and, Data sharing, évolution génomique, Salmonid fish
Abstract: We describe an emerging initiative - the ‘Functional Annotation of All Salmonid Genomes’ (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic variation. The outcomes of FAASG will have diverse applications, ranging from improved understanding of genome evolution, to improving the efficiency and sustainability of aquaculture production, supporting the future of fundamental and applied research in an iconic fish lineage of major societal importance. © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/)
Published: 2017
Full Text: View/download PDF

8. The future of transposable element annotation and their classification in the light of functional genomics - what we can learn from the fables of Jean de la Fontaine?

Author: Peter Arensburger, Yves Bigot, Benoît Piégu, Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Centre National de la Recherche Scientifique (CNRS)-Université de Tours-Institut Français du Cheval et de l'Equitation [Saumur]-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS), California State Polytechnic University, CNRS, INRA, STUDIUM the Groupement de Recherche CNRS 2157, Ministère de l’Education Nationale, de la Recherche et de la Technologie, and Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Transposable element, Retroelements, taxonomie, [SDV]Life Sciences [q-bio], génomique fonctionnelle, repeat, Classification scheme, Biology, commentaire, 010603 evolutionary biology, 01 natural sciences, Biochemistry, Genome, Inteins, Evolution, Molecular, taxonomy, 03 medical and health sciences, Annotation, Commentaries, Terminology as Topic, Genetics, ontology, élément transposable, genome, ontologie, ComputingMilieux_MISCELLANEOUS, [SDV.GEN]Life Sciences [q-bio]/Genetics, Base Sequence, mobile genetic element, Gene Annotation, Sequence Analysis, DNA, Classification, Data science, Introns, 030104 developmental biology, DNA Transposable Elements, Functional genomics, Autre (Sciences du Vivant)
Abstract: The increase of publicly available sequencing data has allowed for rapid progress in our understanding of genome composition. As new information becomes available we should constantly be updating and reanalyzing existing and newly acquired data. In this report we focus on transposable elements (TEs) which make up a significant portion of nearly all sequenced genomes. Our ability to accurately identify and classify these sequences is critical to understanding their impact on host genomes. At the same time, as we demonstrate in this report, problems with existing classification schemes have led to significant misunderstandings of the evolution of both TE sequences and their host genomes. In a pioneering publication Finnegan (1989) proposed classifying all TE sequences into two classes based on transposition mechanisms and structural features: the retrotransposons (class I) and the DNA transposons (class II). We have retraced how ideas regarding TE classification and annotation in both prokaryotic and eukaryotic scientific communities have changed over time. This has led us to observe that: (1) a number of TEs have convergent structural features and/or transposition mechanisms that have led to misleading conclusions regarding their classification, (2) the evolution of TEs is similar to that of viruses by having several unrelated origins, (3) there might be at least 8 classes and 12 orders of TEs including 10 novel orders. In an effort to address these classification issues we propose: (1) the outline of a universal TE classification, (2) a set of methods and classification rules that could be used by all scientific communities involved in the study of TEs, and (3) a 5-year schedule for the establishment of an International Committee for Taxonomy of Transposable Elements (ICTTE).
Published: 2016
Full Text: View/download PDF

9. Genomics tools available for unravelling mechanisms underlying agronomical traits in strawberry with more to come

Author: Kevin M. Folta, Sonia Osorio, Iraida Amaya, Timo Hytönen, Janet P. Slovin, Nahla V. Bassil, Aaron Liston, Richard J. Harrison, Tia-Lynn Ashman, E. van de Weg, Amparo Monfort, Vance M. Whitaker, Béatrice Denoyes, Jacob A. Tennessen, Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA), Oregon State University (OSU), University of Pittsburgh (PITT), Pennsylvania Commonwealth System of Higher Education (PCSHE), Gulf Coast Research and Education Center, University of Helsinki, Plant Research International, Wageningen University and Research Centre [Wageningen] (WUR), Universidad de Málaga [Málaga], University of Florida [Gainesville], United States Department of Agriculture, East Malling Research, IRTA, USDA-ARS : Agricultural Research Service, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Wageningen University and Research [Wageningen] (WUR), Universidad de Málaga [Málaga] = University of Málaga [Málaga], University of Florida [Gainesville] (UF), Desjardins, Y, Strawberry research group, Viikki Plant Science Centre (ViPS), Department of Agricultural Sciences, and Plant Production Sciences
Subjects: 0106 biological sciences, 0301 basic medicine, Population, génomique fonctionnelle, Omics, Genomics, Computational biology, fragaria, Horticulture, Biology, Fragaria, 01 natural sciences, Genome, Polyploidy, PBR Biodiversiteit en Genetische Variatie, 03 medical and health sciences, physiologie végétale, plante fruitière, fraise, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, education, polyploidy, Synteny, 2. Zero hunger, Genetics, Whole genome sequencing, education.field_of_study, 1184 Genetics, developmental biology, physiology, Functional genomics, 414 Agricultural biotechnology, PE&RC, omics, 030104 developmental biology, orchard crops, EPS, strawberry, PBR Biodiversity and genetic variation, functional genomics, 010606 plant biology & botany, Personal genomics, Reference genome
Abstract: UMR 1332 - Equipe OrFE; In the last few years, high-throughput genomics promised to bridge the gap between plant physiology and plant sciences. In addition, high-throughput genotyping technologies facilitate marker-based selection for better performing genotypes. In strawberry, Fragaria vesca was the first reference sequence obtained in the Rosoideae sub-family. This genome has a high level of synteny with genomes of other species of diploid and polyploid Fragaria, but it also provides a reference for species like Rubus and Rosa for functional genomics. Many tools for genetic, genomic and functional analyses were introduced over the last 10 years and these tools are still evolving. For genotyping, many studies have used simple sequence repeats (SSRs) but whole genome sequencing is now a mature technology and facilitates the development of genotyping chips and other genetic approaches such as genome wide association studies (GWAS). Furthermore, microarray-based technologies have been eclipsed by RNA-seq, the high-throughput sequencing of RNA. These new approaches have led to advances in our understanding of the genetically complex octoploid species, and have revolutionized functional genomics. For all genetic and genomic studies, novel material such as complex crosses such as NILs and EMS have appeared in addition to the classical segregating population. With all these tools, strawberry now emerges as a plant model, not only for studying fruit quality but also for deciphering the mechanisms controlling various aspects of plant biology. Selective examples will be described to illustrate the latest research on strawberry and what is coming from other model species.
Published: 2016
Full Text: View/download PDF

10. Transcriptomic Profiling of Egg Quality in Sea Bass (Dicentrarchus labrax) Sheds Light on Genes Involved in Ubiquitination and Translation

Author: Aurélie Le Cam, Julien Bobe, Gilbert Dutto, Daniel Żarski, Marie Odile Vidal, Christian Fauvel, Thuy Thao Vi Nguyen, Jérôme Montfort, Department of Lake and River Fisheries, University of Warmia and Mazury, Department of Aquaculture, Szent István University, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie]), Université de Montpellier (UM), This work was supported by the French National Research Agency (ANR-13-BSV7-0015-Maternal Legacy to JB and CF) and by COST Action (FA1205 AQUAGAMETE), Department of Aquaculture, Szent István University, Gödöllő, Hungary, Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Recherche Agronomique (INRA), ANR-13-BSV7-0015,Maternal Legacy,Portait moléculaire d'un oeuf de poisson de bonne qualité(2013), European Project: COST Action FA 1205, AQUAGAMETE, and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD)
Subjects: 0301 basic medicine, Male, Microarray, DNA Repair, Zygote, [SDV]Life Sciences [q-bio], génomique fonctionnelle, Aquaculture, Applied Microbiology and Biotechnology, bar, Transcriptome, oeuf de poisson, poisson, Controlled reproduction, compétence ovocytaire, foetal development, Oligonucleotide Array Sequence Analysis, Genetics, 04 agricultural and veterinary sciences, Genomics, ovogenèse, contrôle de la reproduction, Real-time polymerase chain reaction, analyse microarray, Dicentrarchus, Female, Original Article, dicentrarchus labrax, sea bass, Biotechnology, expression des gènes, Fish Proteins, qualité des oeufs, processus biologique, Biology, Aquatic Science, reproduction, 03 medical and health sciences, Animals, 14. Life underwater, Sea bass, analyse du transcriptome, Transcriptomics, Gene, fish, Gene Expression Profiling, CENPF, DNA Helicases, Ubiquitination, Molecular Sequence Annotation, biology.organism_classification, moronidae, Protein ubiquitination, Fishery, 030104 developmental biology, Gene Ontology, développement embryonnaire, Protein Biosynthesis, 040102 fisheries, biology.protein, 0401 agriculture, forestry, and fisheries, Bass, microarray analysis, Genetic Fitness, Protein Processing, Post-Translational
Abstract: Variable and low egg quality is a major limiting factor for the development of efficient aquaculture production. This stems from limited knowledge on the mechanisms underlying egg quality in cultured fish. Molecular analyses, such as transcriptomic studies, are valuable tools to identify the most important processes modulating egg quality. However, very few studies have been devoted to this aspect so far. Within this study, the microarray-based transcriptomic analysis of eggs (of different quality) of sea bass (Dicentrarchus labrax) was performed. An Agilent oligo microarray experiment was performed on labelled mRNA extracted from 16 batches of eggs (each batch obtained from a different female) of sea bass, in which over 24,000 published probe arrays were used. We identified 39 differentially expressed genes exhibiting a differential expression between the groups of low (fertilization rate < 60 %) and high (fertilization rate > 60 %) quality. The mRNA levels of eight genes were further analyzed by quantitative PCR. Seven genes were confirmed by qPCR to be differentially expressed in eggs of low and high quality. This study confirmed the importance of some of the genes already reported to be potential molecular quality indicators (mainly rnf213 and irf7), but we also found new genes (mainly usp5, mem-prot, plec, cenpf), which had not yet been reported to be quality-dependent in fish. These results suggest the importance of genes involved in several important processes, such as protein ubiquitination, translation, DNA repair, and cell structure and architecture; these probably being the mechanisms that contribute to egg developmental competence in sea bass.
Published: 2016
Full Text: View/download PDF

11. Petunia, Your Next Supermodel?

Author: Patrice Morel, Suzanne Rodrigues Bento, Pierre Chambrier, Michiel Vandenbussche, Reproduction et développement des plantes (RDP), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), École normale supérieure - Lyon (ENS Lyon), CNRS/ATIP AVENIR award, Agence Nationale de Recherche (ANR BLANC), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), École normale supérieure de Lyon (ENS de Lyon), and Vandenbussche, Michiel
Subjects: transposon mutagenesis, 0106 biological sciences, 0301 basic medicine, evo–devo, genome sequence, [SDV]Life Sciences [q-bio], media_common.quotation_subject, génomique fonctionnelle, Gene regulatory network, Context (language use), Plant Science, Comparative biology, lcsh:Plant culture, 01 natural sciences, 03 medical and health sciences, Arabidopsis, evolution, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, mutagénèse par insertion, lcsh:SB1-1110, petunia, Function (engineering), Clade, media_common, Genetics, biology, plants, model system, functional genomics, evo-devo, 15. Life on land, biology.organism_classification, séquence du génome, 030104 developmental biology, Evolutionary biology, Perspective, Evolutionary developmental biology, modèle dynamique, Functional genomics, 010606 plant biology & botany
Abstract: International audience; Plant biology in general, and plant evo-devo in particular would strongly benefit from a broader range of available model systems. In recent years, technological advances have facilitated the analysis and comparison of individual gene functions in multiple species, representing now a fairly wide taxonomic range of the plant kingdom. Because genes are embedded in gene networks, studying evolution of gene function ultimately should be put in the context of studying the evolution of entire gene networks, since changes in the function of a single gene will normally go together with further changes in its network environment. For this reason, plant comparative biology/evo-devo will require the availability of a defined set of 'super' models occupying key taxonomic positions, in which performing gene functional analysis and testing genetic interactions ideally is as straightforward as, e.g., in Arabidopsis. Here we review why petunia has the potential to become one of these future supermodels, as a representative of the Asterid Glade. We will first detail its intrinsic qualities as a model system. Next, we highlight how the revolution in sequencing technologies will now finally allows exploitation of the petunia system to its full potential, despite that petunia has already a long history as a model in plant molecular biology and genetics. We conclude with a series of arguments in favor of a more diversified multi-model approach in plant biology, and we point out where the petunia model system may further play a role, based on its biological features and molecular toolkit.
Published: 2016
Full Text: View/download PDF

12. Construction of a restriction-less, marker-less mutant useful for functional genomic and metabolic engineering of the biofuel producer Clostridium acetobutylicum

Author: Philippe Soucaille, Maria Gonzalez-Pajuelo, Christian Croux, Florence Saint-Prix, Ngoc-Phuong-Thao Nguyen, Isabelle Meynial-Salles, Céline Raynaud, Jieun Lee, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), College of Life Sciences and Biotechnology, Korea University, Metabolic Explorer, Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), European Project: 237942,EC:FP7:PEOPLE,FP7-PEOPLE-ITN-2008,CLOSTNET(2009), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Korea University [Seoul], and Soucaille, Philippe
Subjects: 0301 basic medicine, Clostridium acetobutylicum, FLP, Mutant, génomique fonctionnelle, Management, Monitoring, Policy and Law, 7. Clean energy, Applied Microbiology and Biotechnology, Gene replacement, upp gene, Metabolic engineering, 03 medical and health sciences, ingénierie métabolique, Plasmid, resistance gene, Recombinase, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, 5-FU, Génie des procédés, Gene, Genetics, biology, Gene deletion, Renewable Energy, Sustainability and the Environment, Research, Microbiology and Parasitology, séquence d'adn, upp, gène de résistance, biology.organism_classification, Cac824I, Microbiologie et Parasitologie, gene deletion, gene replacement, FRT, Restriction enzyme, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 030104 developmental biology, General Energy, Process Engineering, Biochemistry, biocarburant, bactérie anaérobie, biofuel, metabolic engineering, Functional genomics, Biotechnology
Abstract: Background: Clostridium acetobutylicum is a gram-positive, spore-forming, anaerobic bacterium capable of converting various sugars and polysaccharides into solvents (acetone, butanol, and ethanol). The sequencing of its genome has prompted new approaches to genetic analysis, functional genomics, and metabolic engineering to develop industrial strains for the production of biofuels and bulk chemicals.Results: The method used in this paper to knock-out or knock-in genes in C. acetobutylicum combines the use of an antibiotic-resistance gene for the deletion or replacement of the target gene, the subsequent elimination of the antibiotic-resistance gene with the flippase recombinase system from Saccharomyces cerevisiae, and a C. acetobutylicum strain that lacks upp, which encodes uracil phosphoribosyl-transferase, for subsequent use as a counter-selectable marker. A replicative vector containing (1) a pIMP13 origin of replication from Bacillus subtilis that is functional in Clostridia, (2) a replacement cassette consisting of an antibiotic resistance gene (MLS R ) flanked by two FRT sequences, and (3) two sequences homologous to selected regions around target DNA sequence was first constructed. This vector was successfully used to consecutively delete the Cac824I restriction endonuclease encoding gene (CA_C1502) and the upp gene (CA_C2879) in the C. acetobutylicum ATCC824 chromosome. The resulting C. acetobutylicum Δcac1502Δupp strain is marker-less, readily transformable without any previous plasmid methylation and can serve as the host for the “marker-less” genetic exchange system. The third gene, CA_C3535, shown in this study to encode for a type II restriction enzyme (Cac824II) that recognizes the CTGAAG sequence, was deleted using an upp/5-FU counter-selection strategy to improve the efficiency of the method. The restriction-less marker-less strain and the method was successfully used to delete two genes (ctfAB) on the pSOL1 megaplasmid and one gene (ldhA) on the chromosome to get strains no longer producing acetone or l-lactate.Conclusions: The restriction-less, marker-less strain described in this study, as well as the maker-less genetic exchange coupled with positive selection, will be useful for functional genomic studies and for the development of industrial strains for the production of biofuels and bulk chemicals.
Published: 2016
Full Text: View/download PDF

13. Characterization of an extensive rainbow trout miRNA transcriptome by next generation sequencing

Author: Christine Gaspin, Julien Bobe, Philippe Bardou, Olivier Rué, Jean-Charles Gabillard, Yann Guiguen, Amélie Juanchich, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Recherche Agronomique (INRA), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), The project was founded by INRA (AIP Bioressources 2010 « microTrout » and PHASE division grant « microFish »), by France Génomique National infrastructure, funded as part of ' Investissement d’avenir ' program managed by Agence Nationale pour la Recherche (contrat ANR-10-INBS-09), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Juanchich, Amélie, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], and Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )
Subjects: 0301 basic medicine, animal diseases, [SDV]Life Sciences [q-bio], génomique fonctionnelle, MiRBase, Transcriptome, poisson, salmonids, Genetics, Regulation of gene expression, salmonidae, trout, oncorhynchus mykiss, microRNA, repertoire, High-Throughput Nucleotide Sequencing, rainbow trout, microRNAs, Trout, micro arn, expression tissulaire, DNA microarray, transcription, Biotechnology, Research Article, endocrine system, tissue expression, gene regulation, animal structures, organe, Biology, digestive system, DNA sequencing, reproduction, 03 medical and health sciences, rainbow, séquençage, organ, Animals, 14. Life underwater, Salmonidae, analyse de tissu, fish, Sequence Analysis, RNA, urogenital system, biology.organism_classification, 030104 developmental biology, Rainbow trout, régulation génique, transcriptome, truite arc en ciel
Abstract: Background MicroRNAs (miRNAs) have emerged as important post-transcriptional regulators of gene expression in a wide variety of physiological processes. They can control both temporal and spatial gene expression and are believed to regulate 30 to 70 % of the genes. Data are however limited for fish species, with only 9 out of the 30,000 fish species present in miRBase. The aim of the current study was to discover and characterize rainbow trout (Oncorhynchus mykiss) miRNAs in a large number of tissues using next-generation sequencing in order to provide an extensive repertoire of rainbow trout miRNAs. Results A total of 38 different samples corresponding to 16 different tissues or organs were individually sequenced and analyzed independently in order to identify a large number of miRNAs with high confidence. This led to the identification of 2946 miRNA loci in the rainbow trout genome, including 445 already known miRNAs. Differential expression analysis was performed in order to identify miRNAs exhibiting specific or preferential expression among the 16 analyzed tissues. In most cases, miRNAs exhibit a specific pattern of expression in only a few tissues. The expression data from sRNA sequencing were confirmed by RT-qPCR. In addition, novel miRNAs are described in rainbow trout that had not been previously reported in other species. Conclusion This study represents the first characterization of rainbow trout miRNA transcriptome from a wide variety of tissue and sets an extensive repertoire of rainbow trout miRNAs. It provides a starting point for future studies aimed at understanding the roles of miRNAs in major physiological process such as growth, reproduction or adaptation to stress. These rainbow trout miRNAs repertoire provide a novel resource to advance genomic research in salmonid species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2505-9) contains supplementary material, which is available to authorized users.
Published: 2016
Full Text: View/download PDF

14. Phylogenetic-Derived Insights into the Evolution of Sialylation in Eukaryotes: Comprehensive Analysis of Vertebrate β-Galactoside α2,3/6-Sialyltransferases (ST3Gal and ST6Gal)

Author: Daniel Petit, Roxana Elin Teppa, Olga Plechakova, Anne Harduin-Lepers, Virginie Cogez, Fundación Instituto Leloir, Unité de Génétique Moléculaire Animale (UGMA), Université de Limoges (UNILIM)-Institut National de la Recherche Agronomique (INRA), Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Université Lille Nord de France (COMUE), Fundación Instituto Leloir [Buenos Aires], Unité de Génétique Moléculaire Animale (UMR GMA), Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Centre National de La Recherche Scientifique (CNRS), University of Lille Nord de France (PPF bioinformatique of the Lille1 University), Agence Nationale de la Recherche ANR-2010-BLAN-120401, Ligue regionale de la recherche contre le cancer, CNRS, Université de Lille, Unité de Génétique Moléculaire Animale [UMR GMA], Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 [UGSF], Institut National de la Recherche Agronomique (INRA)-Université de Limoges (UNILIM), and Institut National de la Recherche Agronomique (INRA)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Chimie analytique, génomique fonctionnelle, Review, sialyltransferases, biosynthèse, purl.org/becyt/ford/1 [https], lcsh:Chemistry, chemistry.chemical_compound, Structural bioinformatics, acide sialique, lcsh:QH301-705.5, Spectroscopy, Phylogeny, Phylogenetic tree, evolution, sialic acid, molecular phylogeny, functional genomics, Vertebrate, eucaryote, General Medicine, Bioquímica y Biología Molecular, Computer Science Applications, Biochemistry, Vertebrates, Functional genomics, CIENCIAS NATURALES Y EXACTAS, MOLECULAR PHYLOGENY, Computational biology, Biology, Catalysis, Ciencias Biológicas, Inorganic Chemistry, 03 medical and health sciences, biology.animal, phylogénie moléculaire, FUNCTIONAL GENOMICS, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Physical and Theoretical Chemistry, purl.org/becyt/ford/1.6 [https], SIALIC ACID, Molecular Biology, Gene, Comparative genomics, Organic Chemistry, EVOLUTION, SIALYLTRANSFERASES, N-Acetylneuraminic Acid, Sialic acid, carbohydrates (lipids), 030104 developmental biology, chemistry, lcsh:Biology (General), lcsh:QD1-999, Analytical chemistry, Function (biology)
Abstract: Cell surface of eukaryotic cells is covered with a wide variety of sialylated molecules involved in diverse biological processes and taking part in cell-cell interactions. Although the physiological relevance of these sialylated glycoconjugates in vertebrates begins to be deciphered, the origin and evolution of the genetic machinery implicated in their biosynthetic pathway are poorly understood. Among the variety of actors involved in the sialylation machinery, sialyltransferases are key enzymes for the biosynthesis of sialylated molecules. This review focus on β-galactoside α2,3/6-sialyltransferases belonging to the ST3Gal and ST6Gal families. We propose here an outline of the evolutionary history of these two major ST families. Comparative genomics, molecular phylogeny and structural bioinformatics provided insights into the functional innovations in sialic acid metabolism and enabled to explore how ST-gene function evolved in vertebrates. Fil: Teppa, Roxana Elin. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina Fil: Petit, Daniel. Université de Limoges; Francia Fil: Plechakova, Olga. Universite Lille; Francia. Centre National de la Recherche Scientifique; Francia Fil: Cogez, Virginie. Universite Lille; Francia. Centre National de la Recherche Scientifique; Francia Fil: Harduin-Lepers, Anne. Universite Lille; Francia. Centre National de la Recherche Scientifique; Francia
Published: 2015
Full Text: View/download PDF

15. Expanding Duplication of Free Fatty Acid Receptor-2 (GPR43) Genes in the Chicken Genome

Author: Pascal Froment, Philippe Monget, Sophie Leroux, Isabelle Callebaut, Camille Meslin, Florence Gondret, Christophe Klopp, Sandrine Lagarrigue, Edith Guilbert, Colette Désert, Frédérique Pitel, Pascal G.P. Martin, Anis Djari, Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Centre National de la Recherche Scientifique (CNRS)-Université de Tours-Institut Français du Cheval et de l'Equitation [Saumur]-Institut National de la Recherche Agronomique (INRA), Université Francois Rabelais [Tours], Institut Francais du Cheval et de l’Equitation, UMR 1348 Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage, Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST-Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Institut National de la Recherche Agronomique (INRA)-Génétique animale (G.A.)-Physiologie Animale et Systèmes d'Elevage (PHASE), Institut National de la Recherche Agronomique (INRA), Institut de minéralogie, de physique des matériaux et de cosmochimie (IMPMC), Institut de recherche pour le développement [IRD] : UR206-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC), INRA, INRA, BIA, Unité de Biométrie et Intelligence Artificielle de Toulouse [Castanet-Tolosan] (UBIA), Institut National de la Recherche Agronomique (INRA)-Plateforme bioinformatique du GIS GENOTOUL - Génopole Toulouse Midi-Pyrénées, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Unité de recherche Pharmacologie-Toxicologie (UPT), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Institut Français du Cheval et de l'Equitation [Saumur], Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de recherche pour le développement [IRD] : UR206-Centre National de la Recherche Scientifique (CNRS), Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), ANT FATINTEGER - ANR EpiBird, Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur] (IFCE)-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Institut Français du Cheval et de l'Equitation [Saumur] (IFCE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de recherche pour le développement [IRD] : UR206-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Nonsynonymous substitution, Male, animal structures, Swine, [SDV]Life Sciences [q-bio], chicken, poulet, génomique fonctionnelle, FFAR, Biology, métabolisme des lipides, Genome, Receptors, G-Protein-Coupled, Avian Proteins, Evolution, Molecular, 03 medical and health sciences, régulation, positive selection, Gene Duplication, Gene duplication, evolution, Genetics, Animals, Tissue Distribution, Gene conversion, Copy-number variation, acide gras libre, Gene, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, gene conversion, 0402 animal and dairy science, 04 agricultural and veterinary sciences, 040201 dairy & animal science, genomic DNA, adiposité, duplication, Multigene Family, Female, Synonymous substitution, récepteur, Chickens, Research Article
Abstract: International audience; Free fatty acid receptors (FFAR) belong to a family of five G-protein coupled receptors that are involved in the regulation of lipidmetabolism, so that their loss of function increases the risk of obesity. The aim of this study was to determine the expansion of genesencoding paralogs of FFAR2 in the chicken, considered as amodel organism for developmental biology and biomedical research. Byestimating the gene copy number using quantitative polymerase chain reaction, genomic DNA resequencing, and RNA sequencingdata, we showed the existence of 23 ±1.5 genes encoding FFAR2 paralogs in the chicken genome. The FFAR2 paralogs shared anidentity from 87.2%up to 99%. Extensive gene conversion was responsible for this high degree of sequence similarities betweenthese genes, and this concerned especially the four amino acids known to be critical for ligand binding. Moreover, elevated nonsynonymous/synonymous substitutionratios onsomeamino acids withinor inclose-vicinity of the ligand-bindinggroove suggest thatpositive selectionmay have reduced the effective rate of gene conversion in this region, thus contributing to diversify the function ofsome FFAR2 paralogs. All the FFAR2 paralogs were located on a microchromosome in a same linkage group. FFAR2 genes wereexpressed in different tissues and cells such as spleen, peripheral blood mononuclear cells, abdominal adipose tissue, intestine, andlung, with the highest rate of expression in testis. Further investigations are needed to determine whether these chicken-specificevents along evolution are the consequence of domestication and may play a role in regulating lipid metabolism in this species.
Published: 2015
Full Text: View/download PDF

16. GWAS analyses reveal QTL in egg layers that differ in response to diet differences

Author: Frédéric Herault, Thierry Burlot, Amandine Varenne, Pascale Le Roy, Patrice Dehais, Alain Vignal, Christophe Alleno, Hélène Romé, Hervé Chapuis, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Novogen, Unité de Recherches Avicoles (URA), Institut National de la Recherche Agronomique (INRA), Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Zootests, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Recherches Avicoles (SRA), Syndicats des sélectionneurs avicoles et aquacoles français (SYSAAF), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]
Subjects: production d'oeufs, condition d'élevage, qualité des oeufs, [SDV]Life Sciences [q-bio], Quantitative Trait Loci, génomique fonctionnelle, Single-nucleotide polymorphism, Genome-wide association study, Biology, Quantitative trait locus, Polymorphism, Single Nucleotide, 03 medical and health sciences, Family-based QTL mapping, Genetics, Animals, SNP, Genetics(clinical), Gene–environment interaction, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, qtl, génotype animal, 0402 animal and dairy science, Chromosome Mapping, food and beverages, 04 agricultural and veterinary sciences, General Medicine, poule pondeuse, 040201 dairy & animal science, Genetic architecture, Diet, SNP genotyping, régime alimentaire, Oviparity, Female, Gene-Environment Interaction, Animal Science and Zoology, Chickens, Genome-Wide Association Study, Research Article
Abstract: Background The genetic architecture of egg production and egg quality traits, i.e. the quantitative trait loci (QTL) that influence these traits, is still poorly known. To date, 33 studies have focused on the detection of QTL for laying traits in chickens, but less than 10 genes have been identified. The availability of a high-density SNP (single nucleotide polymorphism) chicken array developed by Affymetrix, i.e. the 600K Affymetrix® Axiom® HD genotyping array offers the possibility to narrow down the localization of previously detected QTL and to detect new QTL. This high-density array is also anticipated to take research beyond the classical hypothesis of additivity of QTL effects or of QTL and environmental effects. The aim of our study was to search for QTL that influence laying traits using the 600K SNP chip and to investigate whether the effects of these QTL differed between diets and age at egg collection. Results One hundred and thirty-one QTL were detected for 16 laying traits and were spread across all marked chromosomes, except chromosomes 16 and 25. The percentage of variance explained by a QTL varied from 2 to 10 % for the various traits, depending on diet and age at egg collection. Chromosomes 3, 9, 10 and Z were overrepresented, with more than eight QTL on each one. Among the 131 QTL, 60 had a significantly different effect, depending on diet or age at egg collection. For egg production traits, when the QTL × environment interaction was significant, numerous inversions of sign of the SNP effects were observed, whereas for egg quality traits, the QTL × environment interaction was mostly due to a difference of magnitude of the SNP effects. Conclusions Our results show that numerous QTL influence egg production and egg quality traits and that the genomic regions, which are involved in shaping the ability of layer chickens to adapt to their environment for egg production, vary depending on the environmental conditions. The next question will be to address what the impact of these genotype × environment interactions is on selection. Electronic supplementary material The online version of this article (doi:10.1186/s12711-015-0160-2) contains supplementary material, which is available to authorized users.
Published: 2015
Full Text: View/download PDF

17. A human-curated annotation of the Candida albicans genome

Author: Gerwald A. Köhler, Ursula Oberholzer, Carol A. Munro, Alexander D. Johnson, Jan Ihmels, Martine Raymond, Dominique Sanglard, Anastasia Levitin, George Newport, Jan Dungan, M. Andrew Uhl, Catherine Bachewich, Edwin Wang, Sadri Znaidi, Michael C. Lorenz, Anne Marcil, Steve Bates, Hervé Hogues, Gavin Sherlock, Bernard Turcotte, Aaron P. Mitchell, Marco van het Hoog, Burkhard R. Braun, Tatiana Iouk, Kim Rutherford, Lionel Frangeul, Lois L. Hoyer, Judith Berman, Fredj Tekaia, Daniel Dignard, Mikhail Martchenko, Malcolm Whiteway, Christophe d'Enfert, Neil A. R. Gow, Nina Agabian, Rosa Zito, Joachim Morschhäuser, Diane O. Inglis, Alan Kuo, Matthew Berriman, André Nantel, Maria C. Costanzo, Doreen Harcus, Department of Microbiology and Immunology, University of California, Biotechnology Research Institute (Environmental Biotechnology Sector), National Research Council of Canada (NRC), Biologie et Pathogénicité fongiques, Institut Pasteur [Paris]-Institut National de la Recherche Agronomique (INRA), Department of stomatology, University of São Paulo (USP), The Wellcome Trust Sanger Institute [Cambridge], University of Texas, Intégration et Analyse Génomique (Plate-Forme 4) (PF4), Institut Pasteur [Paris], Génétique Moléculaire des Levures, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), School of Medical Sciences, University of Aberdeen, University of Illinois System, University of Würzburg, Université de Montréal (UdeM), McGill University = Université McGill [Montréal, Canada], Sanford University School of Medecine, Partenaires INRAE, Department of Molecular Genetics, Weizmann Institute of Science [Rehovot, Israël], Department of Genetics, Cell Biology and Development, University of Minnesota [Twin Cities] (UMN), University of Minnesota System-University of Minnesota System, Institut de Microbiologie, Centre Hospitalier Universitaire Vaudois [Lausanne] (CHUV), Columbia University [New York], University of California [San Francisco] (UCSF), University of California (UC), Biologie et Pathogénicité fongiques (BPF), Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris] (IP), Universidade de São Paulo = University of São Paulo (USP), Institut Pasteur [Paris] (IP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), University of California [San Francisco] (UC San Francisco), and Snyder, Michael
Subjects: Yeast and Fungi, Cancer Research, BIOINFORMATIC, lcsh:QH426-470, Gene prediction, Saccharomyces cerevisiae, génomique fonctionnelle, CATABOLIC RANGE, Genome, Microbiology, GENOME ANNOTATION, 03 medical and health sciences, Genetics, Candida albicans, Molecular Biology, Gene, levure, Genetics (clinical), Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Genetics/Genomics, Comparative genomics, Genetics/Gene Discovery, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, biology, 030306 microbiology, Human Genome, ANTIFUNGAL THERAPY, biology.organism_classification, Corpus albicans, FUNGAL GENOME, 3. Good health, lcsh:Genetics, Infectious Diseases, SHORT TANDEM REPEAT, Identification (biology), candida albicans, Infection, Bioinformatics - Computational Biology, Biotechnology, Developmental Biology, Research Article
Abstract: Recent sequencing and assembly of the genome for the fungal pathogen Candida albicans used simple automated procedures for the identification of putative genes. We have reviewed the entire assembly, both by hand and with additional bioinformatic resources, to accurately map and describe 6,354 genes and to identify 246 genes whose original database entries contained sequencing errors (or possibly mutations) that affect their reading frame. Comparison with other fungal genomes permitted the identification of numerous fungus-specific genes that might be targeted for antifungal therapy. We also observed that, compared to other fungi, the protein-coding sequences in the C. albicans genome are especially rich in short sequence repeats. Finally, our improved annotation permitted a detailed analysis of several multigene families, and comparative genomic studies showed that C. albicans has a far greater catabolic range, encoding respiratory Complex 1, several novel oxidoreductases and ketone body degrading enzymes, malonyl-CoA and enoyl-CoA carriers, several novel amino acid degrading enzymes, a variety of secreted catabolic lipases and proteases, and numerous transporters to assimilate the resulting nutrients. The results of these efforts will ensure that the Candida research community has uniform and comprehensive genomic information for medical research as well as for future diagnostic and therapeutic applications., Synopsis Candida albicans is a commonly encountered fungal pathogen usually responsible for superficial infections (thrush and vaginitis). However, an estimated 30% of severe fungal infections, most due to Candida, result in death. Those who are most at risk include individuals taking immune-suppressive drugs following organ transplantation, people with HIV infection, premature infants, and cancer patients undergoing chemotherapy. Current therapies for this pathogen are made more difficult by the significant secondary effects of anti-fungal drugs that target proteins that are also found in the human host. Recent sequencing and assembly of the genome for the fungal pathogen C. albicans used simple automated procedures for the identification of putative genes. Here, we report a detailed annotation of the 6,354 genes that are present in the genome sequence of this organism, essentially writing the dictionary of the C. albicans genome. Comparison with other fungal genomes permitted the identification of numerous fungus-specific genes that are absent from the human genome and whose products might be targeted for antifungal therapy. The results of these efforts will thus ensure that the Candida research community has uniform and comprehensive genomic information for medical research, for the development of functional genomic tools as well as for future diagnostic and therapeutic applications.
Published: 2005
Full Text: View/download PDF

18. Transcriptome-wide investigation of genomic imprinting in chicken

Author: Bertrand Bed'Hom, Frédérique Pitel, Patrice Dehais, Alain Vignal, Magali San Cristobal, Mireille Morisson, David Gourichon, Catherine Beaumont, Farhad Hormozdiari, Sandrine Lagarrigue, Laure Fresard, Florence Vignoles, Jean-Luc Coville, Sophie Leroux, Tatiana Zerjal, Bertrand Servin, Nathalie Marsaud, Laboratoire de Génétique Cellulaire (LGC), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Pôle d'Expérimentation Avicole de Tours (PEAT), Institut National de la Recherche Agronomique (INRA), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, University of California [Los Angeles] (UCLA), University of California, Recherches Avicoles (SRA), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Department of Computer Sciences, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Pôle d'Expérimentation Avicole de Tours (UE PEAT), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Unité de Recherches Avicoles (URA), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and ProdInra, Archive Ouverte
Subjects: Male, Sequence analysis, [SDV]Life Sciences [q-bio], poulet, génomique fonctionnelle, Chick Embryo, Biology, Quantitative trait locus, Genome, Polymorphism, Single Nucleotide, 03 medical and health sciences, Genomic Imprinting, Mice, épigénétique, 0302 clinical medicine, Genetics, Animals, Imprinting (psychology), Gene, 030304 developmental biology, 0303 health sciences, Sequence Analysis, RNA, Gene Expression Profiling, Haplotype, Gene Expression Regulation, Developmental, High-Throughput Nucleotide Sequencing, Genomics, pyroséquençage, Gene expression profiling, [SDV] Life Sciences [q-bio], Mice, Inbred DBA, Female, empreinte génétique, Genomic imprinting, Transcriptome, Chickens, 030217 neurology & neurosurgery
Abstract: Genomic imprinting is an epigenetic mechanism by which alleles of some specific genes are expressed in a parent-of-origin manner. It has been observed in mammals and marsupials, but not in birds. Until now, only a few genes orthologous to mammalian imprinted ones have been analyzed in chicken and did not demonstrate any evidence of imprinting in this species. However, several published observations such as imprinted-like QTL in poultry or reciprocal effects keep the question open. Our main objective was thus to screen the entire chicken genome for parental-allele-specific differential expression on whole embryonic transcriptomes, using high-throughput sequencing. To identify the parental origin of each observed haplotype, two chicken experimental populations were used, as inbred and as genetically distant as possible. Two families were produced from two reciprocal crosses. Transcripts from 20 embryos were sequenced using NGS technology, producing ∼200 Gb of sequences. This allowed the detection of 79 potentially imprinted SNPs, through an analysis method that we validated by detecting imprinting from mouse data already published. However, out of 23 candidates tested by pyrosequencing, none could be confirmed. These results come together, without a priori, with previous statements and phylogenetic considerations assessing the absence of genomic imprinting in chicken.
Published: 2014
Full Text: View/download PDF

19. Re-sequencing data for refining candidate genes and polymorphisms in QTL regions affecting adiposity in chicken

Author: Anis Djari, Diane Esquerre, Colette Désert, Sandrine Lagarrigue, Christophe Klopp, Morgane Boutin, Olivier Demeure, Pierre-François Roux, Demeure, Olivier, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Université européenne de Bretagne - European University of Brittany (UEB), SIGENAE, Institut National de la Recherche Agronomique (INRA), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: Candidate gene, Heredity, Genetic Linkage, [SDV]Life Sciences [q-bio], génomique fonctionnelle, lcsh:Medicine, tissu adipeux, 0302 clinical medicine, INDEL Mutation, Genome Sequencing, lcsh:Science, Adiposity, Genetics, 0303 health sciences, Multidisciplinary, Chromosome Mapping, High-Throughput Nucleotide Sequencing, food and beverages, Genome project, Genomics, Genetic Mapping, Linkage Analysis, annotation fonctionnelle, Research Article, cartographie de qtl, Genotype, Quantitative Trait Loci, poulet, Single-nucleotide polymorphism, Quantitative trait locus, Biology, Research and Analysis Methods, Polymorphism, Single Nucleotide, 03 medical and health sciences, Genetic linkage, Animals, Obesity, Indel, Molecular Biology Techniques, Sequencing Techniques, Gene, Molecular Biology, Genetic Association Studies, 030304 developmental biology, Evolutionary Biology, Population Biology, High Throughput Sequencing, lcsh:R, Biology and Life Sciences, Computational Biology, Molecular Sequence Annotation, Genome Analysis, Genetic Polymorphism, lcsh:Q, Chickens, 030217 neurology & neurosurgery, Population Genetics
Abstract: In this study, we propose an approach aiming at fine-mapping adiposity QTL in chicken, integrating whole genome re-sequencing data. First, two QTL regions for adiposity were identified by performing a classical linkage analysis on 1362 offspring in 11 sire families obtained by crossing two meat-type chicken lines divergently selected for abdominal fat weight. Those regions, located on chromosome 7 and 19, contained a total of 77 and 84 genes, respectively. Then, SNPs and indels in these regions were identified by re-sequencing sires. Considering issues related to polymorphism annotations for regulatory regions, we focused on the 120 and 104 polymorphisms having an impact on protein sequence, and located in coding regions of 35 and 42 genes situated in the two QTL regions. Subsequently, a filter was applied on SNPs considering their potential impact on the protein function based on conservation criteria. For the two regions, we identified 42 and 34 functional polymorphisms carried by 18 and 24 genes, and likely to deeply impact protein, including 3 coding indels and 4 nonsense SNPs. Finally, using gene functional annotation, a short list of 17 and 4 polymorphisms in 6 and 4 functional genes has been defined. Even if we cannot exclude that the causal polymorphisms may be located in regulatory regions, this strategy gives a complete overview of the candidate polymorphisms in coding regions and prioritize them on conservation- and functional-based arguments.
Published: 2014
Full Text: View/download PDF

20. Des étiquettes pour les gènes : Une revue

Author: François Gasser, François Hatey, Philippe Mulsant, Catherine Clouscard-Martinato, Gwenola Tosser-Klopp, Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: 0106 biological sciences, carte génétique, lcsh:QH426-470, génomique fonctionnelle, Biology, Quantitative trait locus, marqueur, 01 natural sciences, Genome, 03 medical and health sciences, Complementary DNA, Genetics, Genetics(clinical), Gene, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, lcsh:SF1-1100, 030304 developmental biology, 0303 health sciences, Expressed sequence tag, [SDV.GEN]Life Sciences [q-bio]/Genetics, cDNA library, Research, food and beverages, General Medicine, génétique comparée, lcsh:Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Genetic marker, Animal Science and Zoology, lcsh:Animal culture, Function (biology), 010606 plant biology & botany
Abstract: Expressed sequence tags (ESTs) are partial sequences from the extremities of complementary DNA (CDNA) resulting from a single pass sequencing of clones from cDNA libraries, and different ESTs can be obtained from one gene. Sequence information from ESTs can be used for deciphering the function and the organisation of the genome. From a functional viewpoint, they allow the determination of the expression profiles of genes in any particular tissue, in different conditions or status, and thus the identification of regulated genes. In order to identify genes involved in particular processes one can select a specific group of mRNAs. For such a selection, classical techniques include subtraction or differential screening and new techniques, using polymerase chain reaction (PCR) amplification, are now available. For studies on the organisation of the genome the main use of ESTs is the determination of chromosomal localisation of the corresponding genes using a somatic hybrid cell panel. This chromosomal localisation information is needed to identify genes or quantitative trait loci, according to the ’positional candidate’ approach. ESTs also contribute to comparative genetics and they can help to decipher gene function by comparison between species, even genetically distant ones. Thus, combining sequence, functional and localisation data, ESTs contribute to an integrated approach to the genome., Les « étiquettes » correspondent aux séquences des extrémités des ADN complémentaires, obtenues de manière systématique à partir d’une seule réaction de séquençage. Cependant, à partir d’un seul gène plusieurs étiquettes différentes peuvent être obtenues : celles qui correspondent aux deux extrémités de l’ADN complémentaire, aux ADN complémentaires de tailles différentes synthétisés à partir d’un même ARN messager, et aux différents ARN messagers issus d’une même séquence d’ADN génomique. L’identification des gènes correspondants est faite par comparaison avec les séquences nucléiques ou protéiques contenues dans les bases de données publiques (GenBank ou EMBL, SwissProt), en utilisant des logiciels d’alignement automatique tels que FASTA ou BLAST. Les séquences annotées des étiquettes sont stockées dans une base de données particulière, dbEST, et soumises régulièrement à des tests de comparaison avec les bases de données citées. En raison de la présence d’une longue région non codante à l’extrémité 3’ des ARN messagers, les étiquettes de l’extrémité 3’ sont souvent non informatives. La comparaison des étiquettes entre elles permet d’essayer de regrouper celles qui peuvent appartenir à un même gène et de déterminer ainsi une séquence consensus, plus longue et donc plus informative. Au niveau fonctionnel, les étiquettes permettent d’établir les profils d’expression des gènes d’un tissu donné dans différentes situations physiologiques ou expérimentales et donc d’identifier les gènes qui sont régulés. Ces profils sont établis en utilisant les étiquettes pour mesurer la fréquence des différents ADNc dans une génothèque préparée à partir de ce tissu dans les différentes conditions étudiées. Dans une nouvelle stratégie, la SAGE (Serial Analysis of Gene expression), des étiquettes d’une dizaine de nucléotides sont collectées, mises bout à bout et séquencées en série, ce qui permet d’accélérer l’acquisition de ces profils d’expression. Une autre approche est basée sur l’hybridation d’un grand nombre de clones déposés sur une même membrane en nylon «filtres haute densité », ou, dans un format miniature, sur une lame de verre, « microarrays». Pour identifier les gènes impliqués dans des processus bien définis, différentes stratégies de soustraction ou de comparaison permettent de sélectionner une population particulière d’ARN messagers ; les techniques les plus récentes utilisent l’amplification par PCR. Au niveau de l’organisation du génome, les étiquettes contribuent au développement de la cartographie génique : les gènes correspondants sont localisés en utilisant un panel d’hybrides somatiques, les amorces nécessaires pour amplifier l’ADN des hybrides sont choisies grâce aux informations de séquence fournies par les étiquettes. Cette information de localisation chromosomique est indispensable pour identifier les gènes responsables des caractères étudiés par une stratégie de gène candidat positionnel. L’utilisation d’étiquettes d’une autre espèce peut également permettre d’effectuer ces localisations et donc de développer des cartes comparées entre espèces qui mettent en évidence une certaine conservation de l’organisation des gènes sur les chromosomes. Enfin, la conservation des gènes n’est pas limitée à la séquence et à l’organisation : grâce aux étiquettes, des analogies fonctionnelles de gènes appartenant à des espèces génétiquement éloignées ont été décrites et sont recherchées systématiquement pour identifier la fonction des gènes. Ainsi, en permettant de combiner des données de séquence, d’expression et de localisation chromosomique, les étiquettes participent au développement d’une approche intégrée du génome.
Published: 1998

21. Genome-Wide SNP Genotyping to Infer the Effects on Gene Functions in Tomato

Author: Hiroyuki Fukuoka, Sachiko Isobe, Koh Aoki, Satoshi Tabata, Shusei Sato, Christophe Rothan, Hideki Hirakawa, Akio Ohyama, Kenta Shirasawa, Department of Electronics and Electrical Engineering, Faculty of Science and Technology, Keio University, Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Kazusa DNA Research Institute (KDRI), NARO Institute of Vegetable and Tea Science, Partenaires INRAE, Osaka University, and Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1
Subjects: 0106 biological sciences, Genotype, [SDV]Life Sciences [q-bio], Mutation, Missense, génomique fonctionnelle, Sequence Homology, Genomics, Single-nucleotide polymorphism, Breeding, Biology, Genes, Plant, Polymorphism, Single Nucleotide, 01 natural sciences, Genome, Homology (biology), 03 medical and health sciences, tomate, physiologie végétale, Solanum lycopersicum, single nucleotide polymorphism (SNP), Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Molecular Biology, Gene, homology modelling, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 2. Zero hunger, Whole genome sequencing, 0303 health sciences, Vegetal Biology, Chimera, food and beverages, General Medicine, fruit, Full Papers, SNP genotyping, goldengate assay, infinium assay, développement du fruit, Biologie végétale, Genome-Wide Association Study, 010606 plant biology & botany
Abstract: International audience; The genotype data of 7054 single nucleotide polymorphism (SNP) loci in 40 tomato lines, including inbred lines, F1 hybrids, and wild relatives, were collected using Illumina's Infinium and GoldenGate assay platforms, the latter of which was utilized in our previous study. The dendrogram based on the genotype data corresponded well to the breeding types of tomato and wild relatives. The SNPs were classified into six categories according to their positions in the genes predicted on the tomato genome sequence. The genes with SNPs were annotated by homology searches against the nucleotide and protein databases, as well as by domain searches, and they were classified into the functional categories defined by the NCBI's eukaryotic orthologous groups (KOG). To infer the SNPs' effects on the gene functions, the three-dimensional structures of the 843 proteins that were encoded by the genes with SNPs causing missense mutations were constructed by homology modelling, and 200 of these proteins were considered to carry non-synonymous amino acid substitutions in the predicted functional sites. The SNP information obtained in this study is available at the Kazusa Tomato Genomics Database (http://plant1.kazusa.or.jp/tomato/).
Published: 2013
Full Text: View/download PDF

22. Exploration of plant genomes in the FLAGdb++ environment

Author: Franck Samson, Cécile Guichard, Jean-Charles Leplé, Philippe Label, Véronique Brunaud, Sébastien Aubourg, Sandra Derozier, Jean-Philippe Tamby, Alain Lecharny, Séverine Gagnot, Philippe Grevet, Unité Mathématique Informatique et Génome (MIG), Institut National de la Recherche Agronomique (INRA), Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Unité de recherche Amélioration, Génétique et Physiologie Forestières (AGPF), ANR project, Genoplante project, and Aubourg, Sebastien
Subjects: 0106 biological sciences, analyse de données, génomique fonctionnelle, Plant Science, computer.software_genre, 01 natural sciences, Genome, DATA INTEGRATION, GENOME DE LA PLANTE, FUNCTIONAL ANALYSIS, Génétique des plantes, GENOMICS, PLANT GENOME, BIOINFORMATICS, FUNCTIONAL GENOMICS, DATA ANALYSIS, STRUCTURAL ANNOTATION, SYSTEM BIOLOGY, COMPARATIVE GENOMICS, GENOMIQUE, ANALYSE FONCTIONNELLE, INTEGRATION DE DONNEES, ANNOTATION STRUCTURALE, lcsh:QH301-705.5, bioinformatique, computer.programming_language, génomique comparée, 0303 health sciences, food and beverages, analyse comparative, DECIPHER, Data mining, Functional genomics, Biotechnology, Data integration, biologie des systèmes, Java, Systems biology, Genomics, Computational biology, lcsh:Plant culture, Biology, Plants genetics, Database, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Genetics, lcsh:SB1-1110, 030304 developmental biology, Comparative genomics, lcsh:Biology (General), computer, 010606 plant biology & botany
Abstract: Background In the contexts of genomics, post-genomics and systems biology approaches, data integration presents a major concern. Databases provide crucial solutions: they store, organize and allow information to be queried, they enhance the visibility of newly produced data by comparing them with previously published results, and facilitate the exploration and development of both existing hypotheses and new ideas. Results The FLAGdb++ information system was developed with the aim of using whole plant genomes as physical references in order to gather and merge available genomic data from in silico or experimental approaches. Available through a JAVA application, original interfaces and tools assist the functional study of plant genes by considering them in their specific context: chromosome, gene family, orthology group, co-expression cluster and functional network. FLAGdb++ is mainly dedicated to the exploration of large gene groups in order to decipher functional connections, to highlight shared or specific structural or functional features, and to facilitate translational tasks between plant species (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa and Vitis vinifera). Conclusion Combining original data with the output of experts and graphical displays that differ from classical plant genome browsers, FLAGdb++ presents a powerful complementary tool for exploring plant genomes and exploiting structural and functional resources, without the need for computer programming knowledge. First launched in 2002, a 15th version of FLAGdb++ is now available and comprises four model plant genomes and over eight million genomic features.
Published: 2011
Full Text: View/download PDF

23. Analysis of virion structural components reveals vestiges of the ancestral ichnovirus genome

Author: Fabrice Legeai, Gabor Gyapay, Fasséli Coulibaly, Patrick Wincker, Anne-Nathalie Volkoff, Catherine Béliveau, Jean-Michel Drezen, Sylvie Samain, Max Bergoin, Véronique Jouan, François Cousserans, Serge Urbach, Bertille Provost, Michel Cusson, Edith Demettre, Biologie Intégrative et Virologie des Insectes [Univ. de Montpellier II] (BIVI), Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), Institut de Génomique Fonctionnelle (IGF), Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), BioCampus Montpellier (BCM), Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Structural Virology Group, Monash University [Clayton], Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Biological systems and models, bioinformatics and sequences (SYMBIOSE), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), Laurentian Forestry Centre, Natural Resources Canada (NRCan), Institut de recherche sur la biologie de l'insecte UMR7261 (IRBI), Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), ANR-05-BLAN-0199,EVPARASITOID,Physiologie, diversité et évolution des interactions hôte-parasitoïde(2005), ANR-09-BLAN-0243,PARATOXOSE(2009), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Université de Tours-Centre National de la Recherche Scientifique (CNRS), ANR-09-BLAN-0243,PARATOXOSE,Parasitoid Toxins : Origin, Specificity, Evolution(2009), Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Virologie moléculaire et structurale (VMS), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Legeai, Fabrice, Programme non thématique - Appel à projets de recherche - Physiologie, diversité et évolution des interactions hôte-parasitoïde - - EVPARASITOID2005 - ANR-05-BLAN-0199 - BLANC - VALID, Blanc - - PARATOXOSE2009 - ANR-09-BLAN-0243 - Blanc - VALID, AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, Genome, Insect, Wasps, génomique fonctionnelle, 01 natural sciences, Genome, Nudivirus, chemistry.chemical_compound, Proviruses, hyposoter didymator, Convergent evolution, lcsh:QH301-705.5, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], Genetics, 0303 health sciences, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], noctuelle, biology, Virulence, Polydnavirus, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Virology/Virus Evolution and Symbiosis, 3. Good health, Multigene Family, ENDOPARASITOIDE LARVAIRE, Female, polydnavirus, Bracovirus, Research Article, lcsh:Immunologic diseases. Allergy, food.ingredient, Immunology, virus, Genome, Viral, macromolecular substances, 010603 evolutionary biology, Microbiology, Evolution, Molecular, 03 medical and health sciences, Viral Proteins, food, Virology, Animals, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Molecular Biology, Gene, 030304 developmental biology, RELATION HOTE-PARASITE, STRUCTURE DU GENOME, VIRUS SYMBIOTIQUE, Ovary, fungi, Virion, biology.organism_classification, chemistry, lcsh:Biology (General), Polydnaviridae, Parasitology, Ichnovirus, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], lcsh:RC581-607, DNA
Abstract: Many thousands of endoparasitic wasp species are known to inject polydnavirus (PDV) particles into their caterpillar host during oviposition, causing immune and developmental dysfunctions that benefit the wasp larva. PDVs associated with braconid and ichneumonid wasps, bracoviruses and ichnoviruses respectively, both deliver multiple circular dsDNA molecules to the caterpillar. These molecules contain virulence genes but lack core genes typically involved in particle production. This is not completely unexpected given that no PDV replication takes place in the caterpillar. Particle production is confined to the wasp ovary where viral DNAs are generated from proviral copies maintained within the wasp genome. We recently showed that the genes involved in bracovirus particle production reside within the wasp genome and are related to nudiviruses. In the present work we characterized genes involved in ichnovirus particle production by analyzing the components of purified Hyposoter didymator Ichnovirus particles by LC-MS/MS and studying their organization in the wasp genome. Their products are conserved among ichnovirus-associated wasps and constitute a specific set of proteins in the virosphere. Strikingly, these genes are clustered in specialized regions of the wasp genome which are amplified along with proviral DNA during virus particle replication, but are not packaged in the particles. Clearly our results show that ichnoviruses and bracoviruses particles originated from different viral entities, thus providing an example of convergent evolution where two groups of wasps have independently domesticated viruses to deliver genes into their hosts., Author Summary The polydnaviruses (PDVs) are a unique virus type used by an organism (a parasitic wasp) to manipulate the physiology of another organism (a lepidopteran host) in order to ensure successful parasitism. The evolutionary origin of these unusual viruses, found in ∼17,500 braconid wasps (Bracoviruses) and ∼15,000 ichneumonid wasps (Ichnoviruses), has been a major question for the last decade. We thus undertook an exclusive work aiming at investigating this origin via the characterization of genes encoding structural components for both types of PDVs. The present paper constitutes the first report on the identity and genome organisation of the viral machinery producing Ichnovirus virions. Our results strongly suggest that Ichnoviruses originated from a virus belonging to a group as yet uncharacterized that integrated its genome into that of an ichneumonid wasp ancestor. More importantly, our results demonstrate that the ancestor of Ichnoviruses differs from that of Bracoviruses, which originated from a nudivirus. We have now identified, for the two types of PDVs, the non packaged viral genes and their products involved in producing particles injected into the host during oviposition. Together, these data provide an example of convergent evolution where different groups of wasps have independently domesticated viruses to deliver genes into their hosts.
Published: 2010
Full Text: View/download PDF

24. Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements

Author: Fabrice Legeai, Philippe Fournier, M. Shimomura, Karl H.J. Gordon, C. Gagneur, Hideki Sezutsu, Emmanuelle Permal, Hadi Quesneville, Arnaud Couloux, Emmanuelle d'Alençon, A. Brun-Barale, Kazuei Mita, René Feyereisen, Sylvie Gimenez, Peter D. East, François Cousserans, Sylvie Bernard-Samain, Timothée Flutre, Biologie Intégrative et Virologie des Insectes [Univ. de Montpellier II] (BIVI), Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), Interactions Biotiques et Santé Végétale, Institut National de la Recherche Agronomique (INRA), National Institute of Agrobiological Sciences (NIAS), National Institute of Agrobiological Sciences, Biological systems and models, bioinformatics and sequences (SYMBIOSE), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Unité de Recherche Génomique Info (URGI), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), CSIRO Entomology [Canberra], CSIRO Entomology, Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: Transposable element, COMPARATIVE GENOMICS, Chromosomes, Artificial, Bacterial, Molecular Sequence Data, génomique fonctionnelle, Genes, Insect, virus, CD13 Antigens, Moths, Biology, syntenie, NOCTUIDAE, Synteny, Genome, Chromosomes, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, Gene duplication, Animals, Cluster Analysis, Gene, 030304 developmental biology, RELATION HOTE-PARASITE, Comparative genomics, Genetics, 0303 health sciences, Multidisciplinary, SILKWORM, STRUCTURE DU GENOME, Base Sequence, fungi, Genomics, Sequence Analysis, DNA, Biological Sciences, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], GENE CLUSTERS, Multigene Family, Holocentric, TRANSPOSABLE ELEMENTS, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], 030217 neurology & neurosurgery, Orthologous Gene
Abstract: The recent assembly of the silkworm Bombyx mori genome with 432 Mb on 28 holocentric chromosomes has become a reference in the genomic analysis of the very diverse Order of Lepidoptera. We sequenced BACs from two major pests, the noctuid moths Helicoverpa armigera and Spodoptera frugiperda , corresponding to 15 regions distributed on 11 B. mori chromosomes, each BAC/region being anchored by known orthologous gene(s) to analyze syntenic relationships and genome rearrangements among the three species. Nearly 300 genes and numerous transposable elements were identified, with long interspersed nuclear elements and terminal inverted repeats the most abundant transposable element classes. There was a high degree of synteny conservation between B. mori and the two noctuid species. Conserved syntenic blocks of identified genes were very small, however, approximately 1.3 genes per block between B. mori and the two noctuid species and 2.0 genes per block between S. frugiperda and H. armigera. This corresponds to approximately two chromosome breaks per Mb DNA per My. This is a much higher evolution rate than among species of the Drosophila genus and may be related to the holocentric nature of the lepidopteran genomes. We report a large cluster of eight members of the aminopeptidase N gene family that we estimate to have been present since the Jurassic. In contrast, several clusters of cytochrome P450 genes showed multiple lineage-specific duplication events, in particular in the lepidopteran CYP9A subfamily. Our study highlights the value of the silkworm genome as a reference in lepidopteran comparative genomics.
Published: 2010
Full Text: View/download PDF

25. The Five AhMTP1 Zinc Transporters Undergo Different Evolutionary Fates towards Adaptive Evolution to Zinc Tolerance in Arabidopsis halleri

Author: Zaigham Shahzad, Nancy Roosens, Pierre Berthomieu, Eric Lacombe, Pierre Saumitou-Laprade, Hélène Frérot, Françoise Gosti, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Génétique et Evolution des Populations Végétales, Université de Lille, Sciences et Technologies-Centre National de la Recherche Scientifique (CNRS), Institut Scientifique de Santé Publique [Belgique] - Scientific Institute of Public Health [Belgium] (WIV-ISP), Réseau International des Instituts Pasteur (RIIP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 0106 biological sciences, Cancer Research, [SDV]Life Sciences [q-bio], Mutant, génomique fonctionnelle, 01 natural sciences, Linkage Disequilibrium, Genetics and Genomics/Plant Genetics and Gene Expression, Plant Biology/Plant Biochemistry and Physiology, Gene Expression Regulation, Plant, Arabidopsis thaliana, Cation Transport Proteins, Genetics (clinical), Phylogeny, Genetics, 0303 health sciences, education.field_of_study, biology, Genetics and Genomics/Functional Genomics, Complementation, Genetics and Genomics/Comparative Genomics, Genome, Plant, Research Article, lcsh:QH426-470, Saccharomyces cerevisiae, Population, chemistry.chemical_element, Plant Biology/Plant-Environment Interactions, Zinc, Evolution, Molecular, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, physiologie végétale, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, transport membranaire, education, Molecular Biology, Gene, Arabidopsis lyrata, Ecology, Evolution, Behavior and Systematics, Genetics and Genomics/Plant Genomes and Evolution, 030304 developmental biology, stress abiotique, [SDV.GEN]Life Sciences [q-bio]/Genetics, Arabidopsis Proteins, tolérance, biology.organism_classification, lcsh:Genetics, arabidopsis, Genetics, Population, chemistry, Carrier Proteins, 010606 plant biology & botany
Abstract: Gene duplication is a major mechanism facilitating adaptation to changing environments. From recent genomic analyses, the acquisition of zinc hypertolerance and hyperaccumulation characters discriminating Arabidopsis halleri from its zinc sensitive/non-accumulator closest relatives Arabidopsis lyrata and Arabidopsis thaliana was proposed to rely on duplication of genes controlling zinc transport or zinc tolerance. Metal Tolerance Protein 1 (MTP1) is one of these genes. It encodes a Zn2+/H+ antiporter involved in cytoplasmic zinc detoxification and thus in zinc tolerance. MTP1 was proposed to be triplicated in A. halleri, while it is present in single copy in A. thaliana and A. lyrata. Two of the three AhMTP1 paralogues were shown to co-segregate with zinc tolerance in a BC1 progeny from a cross between A. halleri and A. lyrata. In this work, the MTP1 family was characterized at both the genomic and functional levels in A. halleri. Five MTP1 paralogues were found to be present in A. halleri, AhMTP1-A1, -A2, -B, -C, and -D. Interestingly, one of the two newly identified AhMTP1 paralogues was not fixed at least in one A. halleri population. All MTP1s were expressed, but transcript accumulation of the paralogues co-segregating with zinc tolerance in the A. halleri X A. lyrata BC1 progeny was markedly higher than that of the other paralogues. All MTP1s displayed the ability to functionally complement a Saccharomyces cerevisiæ zinc hypersensitive mutant. However, the paralogue showing the least complementation of the yeast mutant phenotype was one of the paralogues co-segregating with zinc tolerance. From our results, the hypothesis that pentaplication of MTP1 could be a major basis of the zinc tolerance character in A. halleri is strongly counter-balanced by the fact that members of the MTP1 family are likely to experience different evolutionary fates, some of which not concurring to increase zinc tolerance., Author Summary Arabidopsis halleri has developed the characters of zinc hypertolerance and hyperaccumulation as compared to its close relatives Arabidopsis thaliana and Arabidopsis lyrata. Different candidate genes were proposed to account for the appearance of these characters in A. halleri. One of them is MTP1 (Metal Tolerance Protein 1), which is involved in cytoplasmic zinc detoxification. We found that A. halleri harbored five gene copies of MTP1, whereas A. thaliana and A. lyrata possess a single copy. It is thus tempting to associate the zinc hypertolerance character of A. halleri to the pentaplication of MTP1. However, we observed that one of the five MTP1 copies is not fixed in a population growing on metal contaminated soil. Also, the different MTP1 genes are markedly differentially expressed in A. halleri, two of them being poorly expressed and repressed in response to zinc constraint. AhMTP1 copies were also demonstrated to display a differential ability to complement the zinc hypersensitivity of a yeast mutant that is dysfunctional in vacuolar zinc transporters. Our findings suggest that different evolutionary fates, some of them not concurring to increase zinc tolerance, are likely to take place for the members of the MTP1 family in A. halleri.
Published: 2010
Full Text: View/download PDF

26. Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis

Author: Waltraud X. Schulze, Johann M. Rohwer, Mark Stitt, Björn Usadel, Maria Piques, Yves Gibon, Melanie Höhne, Max Planck Institute of Molecular Plant Physiology (MPI-MP), Max-Planck-Gesellschaft, Station de physiologie végétale, Institut National de la Recherche Agronomique (INRA), and Stellenbosch University
Subjects: 0106 biological sciences, développement végétal, [SDV]Life Sciences [q-bio], Gene Dosage, génomique fonctionnelle, translation, 01 natural sciences, Ribosome, Gene Expression Regulation, Plant, Arabidopsis, Protein biosynthesis, skin and connective tissue diseases, 2. Zero hunger, chemistry.chemical_classification, 0303 health sciences, Applied Mathematics, Translation (biology), Darkness, Circadian Rhythm, ribosome, Computational Theory and Mathematics, Biochemistry, General Agricultural and Biological Sciences, Subcellular Fractions, Information Systems, traduction, RT-PCR QUANTITATIVE, Biology, Article, General Biochemistry, Genetics and Molecular Biology, physiologie végétale, 03 medical and health sciences, Polysome, Respiration, RNA, Messenger, BIOLOGIE VEGETALE, Codon, 030304 developmental biology, polysomes, General Immunology and Microbiology, quantitative RT–PCR, Arabidopsis Proteins, biology.organism_classification, Plant Leaves, arabidopsis, Enzyme, chemistry, Polyribosomes, Protein Biosynthesis, sense organs, polysome, 010606 plant biology & botany
Abstract: Plants are exposed to continual changes in the environment. The daily alternation between light and darkness results in massive recurring changes in the carbon budget, and leads to widespread changes in transcript levels. These diurnal changes are superimposed on slower changes in the environment. Quantitative molecular information about the numbers of ribosomes, of transcripts for 35 enzymes in central metabolism and their loading into polysomes is used to estimate translation rates in Arabidopsis rosettes, and explore the consequences for important sub-processes in plant growth. Translation rates for individual enzyme are compared with their abundance in the rosette to predict which enzymes are subject to rapid turnover every day, and which are synthesized at rates that would allow only slow adjustments to sustained changes of the environment, or resemble those needed to support the observed rate of growth. Global translation rates are used to estimate the energy costs of protein synthesis and relate them to the plant carbon budget, in particular the rates of starch degradation and respiration at night. Molecular Systems Biology 5: 314; published online 13 October 20009; doi:10.1038/msb.2009.68
Published: 2009
Full Text: View/download PDF

27. BMC Genomics

Author: Grace C. Davey, Penelope K. Lindeque, Richard Reinhardt, Christophe Klopp, Pascal Favrel, Dario Moraga, Pierre Boudry, Sylvie Lapegue, Patrick Prunet, Arnaud Huvet, Julien de Lorgeril, Jeanne Moal, Viviane Boulo, Elodie Fleury, Christophe Lelong, Christopher Sauvage, Patrick Wincker, François Moreews, Michel Mathieu, Frédérick Gavory, Arnaud Tanguy, Caroline Fabioux, Charlotte Corporeau, Evelyne Bachère, Jenny P. Shaw, Yannick Gueguen, Laboratoire Environnement Ressources Morbihan Pays de Loire (LERMPL), LITTORAL (LITTORAL), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Physiologie et Ecophysiologie des Mollusques Marins (PE2M), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Ecosystèmes lagunaires : organisation biologique et fonctionnement (ECOLAG), Université Montpellier 2 - Sciences et Techniques (UM2)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Brest (UBO), Plymouth Marine Laboratory (PML), Max-Planck-Institut für Molekulare Genetik (MPIMG), Max-Planck-Gesellschaft, Station commune de Recherches en Ichtyophysiologie, Biodiversité et Environnement (SCRIBE), Institut National de la Recherche Agronomique (INRA), Génétique fonctionnelle, agronomie et santé [IFR 140] (GFAS), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), National Diagnostics Centre (NDC), National University of Ireland [Galway] (NUI Galway), Laboratoire de Génétique et Pathologie (LGP), Amélioration génétique, du contrôle des performances et de la santé des mollusques marins (AGSAE), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Biological systems and models, bioinformatics and sequences (SYMBIOSE), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), Systèmes d'Elevage, Nutrition Animale et Humaine (SENAH), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Rennes, Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), Laboratoire de Physiologie des Invertébrés (LPI), Physiologie Fonctionnelle des Organismes Marins (PFOM), The research presented in this paper was performed within the framework of several research projects funded by: Genoscope (11/AP2006-2007), Marine Genomics Network of Excellence (GOCE-CT-2004-505403), the European project 'Aquafirst' (513692) in the Sixth Framework Program, ANR 'CgPhysiogène' (ANR-06-GANI-0009) and 'Gametogenes' (ANR-08-GENM-041), ANR-06-GANI-0009,CgPhysiogene,Bases moléculaires des fonctions physiologiques de l'huître Crassostrea gigas : interactions hôte/pathogène/milieu(2006), ANR-08-GENM-0041,Gametogenes,Génomiques de la gamétogénèse chez l'huître creuse Crassostrea gigas(2008), Laboratoire Laboratoire Environnement Ressources Morbihan Pays de Loire (LER/MPL), Institut de Recherche pour le Développement (IRD)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS), Adaptation et Biologie des Invertébrés en Conditions Extrêmes (ABICE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Plymouth Marine Laboratory, Institut National de la Recherche Agronomique (INRA)-IFR140, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Ecole Nationale Supérieure Agronomique de Rennes-Institut National de la Recherche Agronomique (INRA), Unité de Biométrie et Intelligence Artificielle de Toulouse [Castanet-Tolosan] (UBIA), Institut National de la Recherche Agronomique (INRA)-Plateforme bioinformatique du GIS GENOTOUL - Génopole Toulouse Midi-Pyrénées, Laboratoire de Physiologie des Invertébrés [Plouzané] (LPI), Adaptation et diversité en milieu marin (AD2M), Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Station biologique de Roscoff (SBR), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Oyster, genome annotation, génomique fonctionnelle, computer.software_genre, Genome, User-Computer Interface, single nucleotide polymorphisms, Databases, Genetic, crassostrea gigas, structure du génome, Expressed Sequence Tags, base de données, 0303 health sciences, Expressed sequence tag, biology, Database, 04 agricultural and veterinary sciences, Genomics, crustacea, Pacific oyster, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], energy-balance, factor-beta superfamily, DNA microarray, expression des gènes, Biotechnology, lcsh:QH426-470, Sequence analysis, lcsh:Biotechnology, kappa-b, Polymorphism, Single Nucleotide, génomique, 03 medical and health sciences, biology.animal, lcsh:TP248.13-248.65, Genetics, summer mortality, Animals, Crassostrea, 030304 developmental biology, Gene Library, Whole genome sequencing, [SDV.GEN]Life Sciences [q-bio]/Genetics, huître, cell-development, génome, Gene Expression Profiling, linkage maps, Sequence Analysis, DNA, biology.organism_classification, lcsh:Genetics, coquillage, 040102 fisheries, 0401 agriculture, forestry, and fisheries, identification, marine genomics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], computer, Microsatellite Repeats
Abstract: Background Although bivalves are among the most-studied marine organisms because of their ecological role and economic importance, very little information is available on the genome sequences of oyster species. This report documents three large-scale cDNA sequencing projects for the Pacific oyster Crassostrea gigas initiated to provide a large number of expressed sequence tags that were subsequently compiled in a publicly accessible database. This resource allowed for the identification of a large number of transcripts and provides valuable information for ongoing investigations of tissue-specific and stimulus-dependant gene expression patterns. These data are crucial for constructing comprehensive DNA microarrays, identifying single nucleotide polymorphisms and microsatellites in coding regions, and for identifying genes when the entire genome sequence of C. gigas becomes available. Description In the present paper, we report the production of 40,845 high-quality ESTs that identify 29,745 unique transcribed sequences consisting of 7,940 contigs and 21,805 singletons. All of these new sequences, together with existing public sequence data, have been compiled into a publicly-available Website http://public-contigbrowser.sigenae.org:9090/Crassostrea_gigas/index.html. Approximately 43% of the unique ESTs had significant matches against the SwissProt database and 27% were annotated using Gene Ontology terms. In addition, we identified a total of 208 in silico microsatellites from the ESTs, with 173 having sufficient flanking sequence for primer design. We also identified a total of 7,530 putative in silico, single-nucleotide polymorphisms using existing and newly-generated EST resources for the Pacific oyster. Conclusion A publicly-available database has been populated with 29,745 unique sequences for the Pacific oyster Crassostrea gigas. The database provides many tools to search cleaned and assembled ESTs. The user may input and submit several filters, such as protein or nucleotide hits, to select and download relevant elements. This database constitutes one of the most developed genomic resources accessible among Lophotrochozoans, an orphan clade of bilateral animals. These data will accelerate the development of both genomics and genetics in a commercially-important species with the highest annual, commercial production of any aquatic organism.
Published: 2009
Full Text: View/download PDF

28. La maîtrise de la tendreté de la viande bovine : identification de marqueurs biologiques

Author: Hubert Levéziel, Gilles Renand, Anne Listrat, Brigitte Picard, Jean-François Hocquette, Nicolas Guillemin, Didier Micol, Isabelle Cassar-Malek, Catherine Jurie, Unité de Recherches sur les Herbivores (URH), Institut National de la Recherche Agronomique (INRA), Unité de Génétique Moléculaire Animale (UMR GMA), Institut National de la Recherche Agronomique (INRA)-Université de Limoges (UNILIM), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité Mixte de Recherches sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA), Unité de Génétique Moléculaire Animale (UGMA), Université de Limoges (UNILIM)-Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherches sur les Herbivores ( UMR 1213 Herbivores ), VetAgro Sup ( VAS ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique ( INRA ), Unité de Génétique Moléculaire Animale ( UGMA ), Université de Limoges ( UNILIM ) -Institut National de la Recherche Agronomique ( INRA ), Génétique Animale et Biologie Intégrative ( GABI ), and Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 0303 health sciences, apoptose, bovin, tendreté, marqueur biologique, viande, fibre musculaire, muscle, 0402 animal and dairy science, génomique fonctionnelle, bovin à viande, 04 agricultural and veterinary sciences, gène marqueur, 040201 dairy & animal science, tendrete, Agricultural sciences, 03 medical and health sciences, protéomique, transcriptome, [ SDV.SA ] Life Sciences [q-bio]/Agricultural sciences, Sciences agricoles, lipide, 030304 developmental biology
Abstract: La tendreté de la viande bovine présente une forte variabilité non maîtrisée qui est à l’origine d’une insatisfaction des consommateurs. De plus, il n’existe pas d’outils fiables et utilisables par la filière bovine pour prédire ce critère de qualité. Depuis de nombreuses années, l’implication des caractéristiques musculaires (collagène, lipides, systèmes protéolytiques, fibres) dans la tendreté a été bien étudiée. Toutefois, lorsque ces caractéristiques sont maîtrisées, il demeure encore une variabilité élevée et non expliquée. Afin d’approfondir les connaissances sur l’origine de cette variabilité, des études de génomique fonctionnelle ont été conduites durant les 10 dernières années. Ces approches permettent de rechercher sans a priori des gènes ou des protéines dont l’expression varie en fonction de la tendreté de la viande. Ces études ont permis d’établir une liste de marqueurs biologiques de la tendreté dont l’analyse phénotypique pourra venir compléter les analyses génétiques de recherche de polymorphismes., Beef tenderness exhibits a high and uncontrolled variability which is one reason for the consumer's dissatisfaction. Moreover, the beef industry does not have predictive tools to measure meat tenderness. During the last few years, the impact of muscular characteristics such as collagen, lipids, proteolytic systems and fibres on meat tenderness has been studied. however, there is still an uncontrolled highly variable meat tenderness even when these muscular characteristics are under control. In order to understand this variability, some genomic studies have been conducted during the last 10 years. They allow the screening, without a priori, of genes and proteins whose expression is variable with meat tenderness. These studies have established a list of tenderness biomarkers whose phenotypic analyses can complete the polymorphism analyses. This article summarises the current knowledge concerning the phenotypic approach, and will be followed by a second article which will present the genetic approach of beef tenderness markers.
Published: 2009

29. UTILLdb, a Pisum sativum in silico forward and reverse genetics tool

Author: Véronique Brunaud, Richard D. Thompson, Abdelhafid Bendahmane, Judith Burstin, Françoise Moussy, Cécile Guichard, Yannick de Oliveira, Christine Le Signor, Marion Dalmais, Julien Schmidt, Grégoire Aubert, Vincent Savois, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), UMR 0102 - Unité de Recherche Génétique et Ecophysiologie des Légumineuses, Génétique et Ecophysiologie des Légumineuses à Graines (UMRLEG) (UMR 102), and Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement
Subjects: 0106 biological sciences, TILLING, Agrobacterium, [SDV]Life Sciences [q-bio], In silico, DNA Mutational Analysis, Mutant, Population, proteagineux, génomique fonctionnelle, Method, Mutagenesis (molecular biology technique), Biology, Genes, Plant, 01 natural sciences, légumineuse, 03 medical and health sciences, Sativum, Databases, Genetic, mutant, education, mutagenèse, Alleles, pisum sativum, 030304 developmental biology, Genetics, 0303 health sciences, education.field_of_study, Peas, food and beverages, biology.organism_classification, Reverse genetics, arabidopsis, Mutagenesis, pois, Ethyl Methanesulfonate, [SDE]Environmental Sciences, mutation, Mutagens, 010606 plant biology & botany
Abstract: UTILLdb is a database of phenotypic and sequence information on mutant genes from a reference Pisum sativum EMS-mutant population., The systematic characterization of gene functions in species recalcitrant to Agrobacterium-based transformation, like Pisum sativum, remains a challenge. To develop a high throughput forward and reverse genetics tool in pea, we have constructed a reference ethylmethane sulfonate mutant population and developed a database, UTILLdb, that contains phenotypic as well as sequence information on mutant genes. UTILLdb can be searched online for TILLING alleles, through the BLAST tool, or for phenotypic information about mutants by keywords.
Published: 2008
Full Text: View/download PDF

30. Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library

Author: Pierre Larmande, Céline Gay, Mathias Lorieux, Christophe Périn, Matthieu Bouniol, Gaëtan Droc, Christophe Sallaud, Pascual Perez, Isabelle Barnola, Corinne Biderre-Petit, Jérôme Martin, Jean Benoît Morel, Alexander A. T. Johnson, Fabienne Bourgis, Alain Ghesquière, Manuel Ruiz, Brigitte Courtois, Emmanuel Guiderdoni, Biologie du développement des espèces pérennes cultivées (UMR BEPC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), CIAT BIOTECHNOLOGY UNIT AA6713, CIAT CALI COLOMBIA, BIOGEMMA, Biogemma Clermont-Ferrand, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Institut d'Astrophysique de Paris (IAP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Laboratoire de Physiologie et de Génétique Moléculaire des Plantes, Université Libre de Bruxelles [Bruxelles] (ULB), Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Développement et amélioration des plantes (UMR DAP), Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), International Center for Tropical Agriculture [Colombie] (CIAT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université libre de Bruxelles (ULB), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Mutant, ADN, Phénotype, génomique fonctionnelle, Banque de gènes, computer.software_genre, 01 natural sciences, F30 - Génétique et amélioration des plantes, User-Computer Interface, céréale, Genes, Reporter, Databases, Genetic, Enhancer trap, Expression des gènes, Genomic library, bioinformatique, ontologie, Sequence Tagged Sites, 2. Zero hunger, Genetics, 0303 health sciences, Database, food and beverages, Articles, Phenotype, C30 - Documentation et information, Système d'information, T-DNA enhancer trap, séquence d'insertion, DNA, Bacterial, Oryza japonica, expression génique, collection de mutant, caractérisation phénotypique, Biology, Sequence-tagged site, 03 medical and health sciences, Oryza tag line database, Gene, 030304 developmental biology, Gene Library, Génie génétique, Reporter gene, Internet, Oryza sativa, RIZ, STRUCTURE DU GENOME, BASE DE DONNEES, Oryza, Phenotypic trait, Mutagenesis, Insertional, oryza sativa, Mutation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, computer, 010606 plant biology & botany
Abstract: UMR DAP, équipe DAR; UMR BGPI, équipe 4; International audience; To organize data resulting from the phenotypic characterization of a library of 30,000 T-DNA enhancer trap (ET) insertion lines of rice (Oryza sativa L cv. Nipponbare), we developed the Oryza Tag Line (OTL) database (http://urgi.versailles.inra.fr/OryzaTagLine/). OTL structure facilitates forward genetic search for specific phenotypes, putatively resulting from gene disruption, and/or for GUSA or GFP reporter gene expression patterns, reflecting ET-mediated endogenous gene detection. In the latest version, OTL gathers the detailed morpho-physiological alterations observed during field evaluation and specific screens in a first set of 13,928 lines. Detection of GUS or GFP activity in specific organ/tissues in a subset of the library is also provided. Search in OTL can be achieved through trait ontology category, organ and/or developmental stage, keywords, expression of reporter gene in specific organ/tissue as well as line identification number. OTL now contains the description of 9721 mutant phenotypic traits observed in 2636 lines and 1234 GUS or GFP expression patterns. Each insertion line is documented through a generic passport data including production records, seed stocks and FST information. 8004 and 6101 of the 13,928 lines are characterized by at least one T-DNA and one Tos17 FST, respectively that OTL links to the rice genome browser OryGenesDB.
Published: 2008
Full Text: View/download PDF

31. OryGenesDB: A database for rice reverse genetics

Author: Droc, Gaëtan, Ruiz, Manuel, Larmande, Pierre, Pereira, Andy, Piffanelli, Pietro, Morel, Jean-Benoit, Dievart, Anne, Courtois, Brigitte, Guiderdoni, Emmanuel, Perin, Christophe, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Polymorphismes d'intérêt agronomique (UMR PIA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Plant Research International (PRI), Wageningen University and Research Centre [Wageningen] (WUR), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Wageningen University and Research [Wageningen] (WUR), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)
Subjects: 0106 biological sciences, génomique fonctionnelle, Genome browser, Banque de gènes, gène marqueur, computer.software_genre, 01 natural sciences, Genome, F30 - Génétique et amélioration des plantes, User-Computer Interface, PRI Biodiversiteit en Veredeling, Databases, Genetic, BANQUE DE GENES, banque de données, Plant Proteins, Sequence Tagged Sites, riz, 2. Zero hunger, Genetics, 0303 health sciences, Database, Chromosome Mapping, food and beverages, Genomics, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], annotation, C30 - Documentation et information, functional genomics, Functional genomics, Genome, Plant, Génétique moléculaire, FLANKING SEQUENCE TAG, Oryza sativa, annotation génomique, Biology, Genes, Plant, Article, REVERSE GENETICS STRATEGIES, Insertional mutagenesis, Sequence-tagged site, 03 medical and health sciences, Pool de gènes, séquençage, FUNCTIONAL GENOMICS, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Gene, 030304 developmental biology, Comparative genomics, Internet, Génome, Mutant, RIZ, Oryza, PRI Biodiversity and Breeding, Mutagenesis, Insertional, système d'information, génétique inverse, resources, computer, 010606 plant biology & botany
Abstract: Insertional mutant databases containing Flanking Sequence Tags (FSTs) are becoming key resources for plant functional genomics. We have developed OryGenesDB(http://orygenesdb.cirad.fr/), a database dedicated to rice reverse genetics. Insertion mutants of rice genes are catalogued by Flanking Sequence Tag (FST) information that can be readily accessed by this database. Our database presently contains 44166 FSTs generated by most of the rice insertional mutagenesis projects. The OryGenesDB genome browser is based on the powerful Generic Genome Browser (GGB) developed in the framework of the Generic Model Organism Project (GMOD). The main interface of our web site displays search and analysis interfaces to look for insertions in any candidate gene of interest. Several starting points can be used to exhaustively retrieve the insertions positions and associated genomic information using blast, keywords or gene name search. The toolbox integrated in our database also includes an 'anchoring' option that allows immediate mapping and visualization of up to 50 nucleic acid sequences in the rice Genome Browser of OryGenesDB. As a first step toward plant comparative genomics, we have linked the rice and Arabidopsis whole genome using all the predicted pairs of orthologs by best BLAST mutual hit (BBMH) connectors.
Published: 2006
Full Text: View/download PDF

32. Characterization of a novel thyroid hormone receptor alpha variant involved in the regulation of myoblast differentiation

Author: Stéphanie Grandemange, Chantal Wrutniak-Cabello, Muriel Busson, Pascal Seyer, Angel Carazo, Laurence Pessemesse, François Casas, Gérard Cabello, Différenciation Cellulaire et Croissance (DCC), and Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)
Subjects: TR ALPHA, Myoblast proliferation, DNA, Complementary, expression génique, Receptors, Retinoic Acid, Molecular Sequence Data, génomique fonctionnelle, Biology, In Vitro Techniques, Quail, Cell Line, Thyroid hormone receptor beta, Myoblasts, 03 medical and health sciences, Mice, Endocrinology, MYOBLAST, Animals, BIOLOGIE DU DEVELOPPEMENT, Tissue Distribution, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, TRANSCRIPTION, Cloning, Molecular, Molecular Biology, 030304 developmental biology, Cell Proliferation, Hormone response element, 0303 health sciences, Thyroid hormone receptor, Base Sequence, 030302 biochemistry & molecular biology, Genetic Variation, Cell Differentiation, General Medicine, Retinoid X receptor gamma, Molecular biology, TRIIODOTHYRONINE, Retinoic acid receptor, Alternative Splicing, Retinoid X Receptors, Nuclear receptor, Thyroid hormone receptor alpha, Gene Expression Regulation, myoblaste, Rabbits, Chickens, Thyroid Hormone Receptors alpha
Abstract: International audience; The regulation of gene expression by thyroid hormone (T-3) involves binding of the hormone to nuclear receptors [ thyroid hormone receptor (TR)] acting as T-3-dependent transcription factors encoded by TR alpha (NR1A1) and TR beta (NR1A2) genes. Several TR alpha variants have already been characterized, but only some of them display T-3 binding activity. In this study, we have identified another transcript, TR alpha-Delta E6, produced by alternative splicing with microexon 6b instead of exon 6. This splicing leads to the synthesis of a protein devoid of a hinge domain. The TR alpha-Delta E6 transcript is detected in all mouse tissues tested. Although TR alpha-Delta E6 did not bind DNA, its expression induced a TR alpha 1 sequestration in the cytoplasm. Functional studies demonstrated that TR alpha-Delta E6 inhibits the transcriptional activity of TR alpha 1 and retinoic X receptor-alpha, but not of retinoic acid receptor-alpha. We also found that TR alpha-Delta E6 efficiently decreased the ability of TR alpha to inhibit MyoD transcriptional activity during myoblast proliferation. Consequently, when overexpressed in myoblasts, it stimulated terminal differentiation. We suggest that this novel TR alpha variant may act as down regulator of overall T-3 receptor activity, including its ability to repress MyoD transcriptional activity during myoblast proliferation.
Published: 2006
Full Text: View/download PDF

33. High-dimensional and large-scale phenotyping of yeast mutants

Author: Yoichiro Nakatani, Satoru Nogami, Fumi Sano, Aiko Hirata, Satomi Oka, Shinichi Morishita, Jean Marie François, Hiroyuki Araki, Markus Aebi, Miwaka Ohtani, Kintake Sonoike, Masashi Yukawa, Tomoyuki Fukuda, Yoshikazu Ohya, Jean-Paul Latgé, Sachiko Muramatsu, Seiji Tanaka, Jim Sese, Genjiro Suzuki, Satoru Ishihara, M. Watanabe, Taro Saito, Nicolas Fraysse, Ayaka Saka, Hiroshi Sawai, Ohya, Yoshikazu, Sese, Jun, Yukawa, Masashi, Aebi, Markus, The University of Tokyo (UTokyo), Japan Science and Technology Corporation, Biologie et Pathogénicité fongiques, Institut Pasteur [Paris]-Institut National de la Recherche Agronomique (INRA), Aspergillus, Institut Pasteur [Paris], Unité mixte de recherche biotechnologies bioprocédés, Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), National Institute of Genetics (NIG), David Botstein, Biologie et Pathogénicité fongiques (BPF), Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris] (IP), Institut Pasteur [Paris] (IP), and Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Time Factors, Genes, Fungal, Saccharomyces cerevisiae, Mutant, HIGH-DIMENSIONAL PHENOTYPING, génomique fonctionnelle, Locus (genetics), [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Quantitative trait locus, Cell morphology, CELL MORPHOLOGY, Fungal Proteins, Open Reading Frames, 03 medical and health sciences, Gene Expression Regulation, Fungal, Yeasts, FUNCTIONAL GENOMICS, GENOME DATABASE, immunofluorescence, Gene, 030304 developmental biology, Cell Nucleus, Recombination, Genetic, Genetics, SACCHAROMYCES CEREVISIAE, 0303 health sciences, Multidisciplinary, Models, Genetic, biology, 030302 biochemistry & molecular biology, Genomics, Biological Sciences, biology.organism_classification, PHENOME, Phenotype, Actins, Yeast, Genetic Techniques, Microscopy, Fluorescence, Mutation, Genome, Fungal, Gene Deletion
Abstract: One of the most powerful techniques for attributing functions to genes in uni- and multicellular organisms is comprehensive analysis of mutant traits. In this study, systematic and quantitative analyses of mutant traits are achieved in the budding yeast Saccharomyces cerevisiae by investigating morphological phenotypes. Analysis of fluorescent microscopic images of triple-stained cells makes it possible to treat morphological variations as quantitative traits. Deletion of nearly half of the yeast genes not essential for growth affects these morphological traits. Similar morphological phenotypes are caused by deletions of functionally related genes, enabling a functional assignment of a locus to a specific cellular pathway. The high-dimensional phenotypic analysis of defined yeast mutant strains provides another step toward attributing gene function to all of the genes in the yeast genome.
Published: 2005
Full Text: View/download PDF

34. Functional genomics in chickens: development of integrated-systems microarrays for transcriptional profiling and discovery of regulatory pathways

Author: Jean Simon, Tom E. Porter, Larry A. Cogburn, L. Rejto, Xin Wang, Samuel E. Aggrey, Michel J. Duclos, Wilfrid Carre, Unité de Recherches Avicoles (URA), and Institut National de la Recherche Agronomique (INRA)
Subjects: animal structures, lcsh:QH426-470, [SDV]Life Sciences [q-bio], consommation alimentaire, poulet, génomique fonctionnelle, Biology, 03 medical and health sciences, régulation, Gene expression, Genetics, oiseau domestique, [INFO]Computer Science [cs], lcsh:Science, lcsh:QH301-705.5, Molecular Biology, Gene, Transcription factor, croissance musculaire, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Expressed sequence tag, Microarray analysis techniques, génome, 0402 animal and dairy science, adn, 04 agricultural and veterinary sciences, 040201 dairy & animal science, volaille, lcsh:Genetics, Metabolic pathway, lcsh:Biology (General), lcsh:Q, DNA microarray, génotype, Functional genomics, Biotechnology, expression des gènes, Research Article
Abstract: The genetic networks that govern the differentiation and growth of major tissues of economic importance in the chicken are largely unknown. Under a functional genomics project, our consortium has generated 30 609 expressed sequence tags (ESTs) and developed several chicken DNA microarrays, which represent the Chicken Metabolic/Somatic (10 K) and Neuroendocrine/Reproductive (8 K) Systems (http://udgenome.ags.udel.edu/cogburn/). One of the major challenges facing functional genomics is the development of mathematical models to reconstruct functional gene networks and regulatory pathways from vast volumes of microarray data. In initial studies with liver-specific microarrays (3.1 K), we have examined gene expression profiles in liver during the peri-hatch transition and during a strong metabolic perturbation—fasting and re-feeding—in divergently selected broiler chickens (fast vs. slow-growth lines). The expression of many genes controlling metabolic pathways is dramatically altered by these perturbations. Our analysis has revealed a large number of clusters of functionally related genes (mainly metabolic enzymes and transcription factors) that control major metabolic pathways. Currently, we are conducting transcriptional profiling studies of multiple tissues during development of two sets of divergently selected broiler chickens (fast vs. slow growing and fat vs. lean lines). Transcriptional profiling across multiple tissues should permit construction of a detailed genetic blueprint that illustrates the developmental events and hierarchy of genes that govern growth and development of chickens. This review will briefly describe the recent acquisition of chicken genomic resources (ESTs and microarrays) and our consortium's efforts to help launch the new era of functional genomics in the chicken.
Published: 2004
Full Text: View/download PDF

35. FLAGdb++: a database for the functional analysis of the Arabidopsis genome

Author: Sylvain Duchêne, Michel Caboche, Yannick de Oliveira, Véronique Brunaud, Alain Lecharny, Franck Samson, Sébastien Aubourg, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, génomique fonctionnelle, Information Storage and Retrieval, Locus (genetics), Computational biology, BASE DE DONNEES, ANALYSE FONCTIONNELLE, 01 natural sciences, Genome, Chromosomes, Plant, 03 medical and health sciences, User-Computer Interface, Arabidopsis, Databases, Genetic, Genetics, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], bioinformatique, 030304 developmental biology, 0303 health sciences, Internet, biology, génome, gène, Experimental data, Computational Biology, Graphical display, Genomics, Articles, biology.organism_classification, Visualization, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], arabidopsis, Arabidopsis genome, Genome, Plant, 010606 plant biology & botany
Abstract: FLAGdb++ is dedicated to the integration and visualization of data for high-throughput functional analysis of a fully sequenced genome, as illustrated for Arabidopsis. FLAGdb++ displays the predicted or experimental data in a position-dependent way and displays correlations and relationships between different features. FLAGdb++ provides for a given genome region, summarized characteristics of experimental materials like probe lengths, locations and specificities having an impact upon the confidence we will put in the experimental results. A selected subset of the available information is linked to a locus represented on an easy-to-interpret and memorable graphical display. Data are curated, processed and formatted before their integration into FLAGdb++. FLAGdb++ contains different options for easy back and forth navigation through many loci selected at the start of a session. It includes an original two-component visualization of the data, a genome-wide and a local view, which are permanently linked and display complementary information. Density curves along the chromosomes may be displayed in parallel for suggesting correlations between different structural and functional data. FLAGdb++ is fully accessible at http://genoplante-info.infobiogen.fr/FLAGdb/.
Published: 2004
Full Text: View/download PDF

36. Gene expression profiling in susceptible interaction of grapevine with its fungal pathogen Eutypa lata: Extending MapMan ontology for grapevine

Author: Claudio Moser, Pierre Coutos-Thévenot, Céline Camps, Serge Delrot, Christian Kappel, Mark Stitt, Ana Rotter, Björn Usadel, S. Pilati, Matjaž Hren, Marc Lohse, Kristina Gruden, Physiologie Moléculaire du Transport des Sucres chez les Végétaux (PhyMoTS), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), and Slovenian Research Agency (Ref. Nos. 1000-05-310172, P4-0165), by the German Ministry of Research and Education (GABI-MAPMEN 0313112/ 0313110), the Fondo Unico of the Provincia Autonoma di Trento, post doc project 'Profiles' (S.P.), and from the Advanced Biology Project funded by the Fondazione delle Casse di Risparmio di Trento e Rovereto
Subjects: 0106 biological sciences, MESH: Xylariales, Microarray, génomique fonctionnelle, Plant Science, champignon pathogène, MESH: RNA, Plant, 01 natural sciences, Genome, phénylpropanoïde, Transcriptome, infection fongique, Gene Expression Regulation, Plant, lcsh:Botany, Gene expression, Vitis, ontologie, Oligonucleotide Array Sequence Analysis, 0303 health sciences, Vegetal Biology, Xylariales, food and beverages, Chromosome Mapping, lcsh:QK1-989, RNA, Plant, puce à adn, Host-Pathogen Interactions, expression des gènes, Research Article, LOGICIEL MAPMAN, expression génique, logiciel, Computational biology, Biology, EUTYPA LATA, MESH: Vitis, 03 medical and health sciences, carotenoide, MESH: Gene Expression Profiling, vitis vinifera, Gene mapping, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, MESH: Gene Expression Regulation, Plant, Gene, 030304 developmental biology, Whole genome sequencing, terpénoïde, business.industry, Gene Expression Profiling, MESH: Host-Pathogen Interactions, fungi, DÉFENSE DES PLANTES, Biotechnology, Gene expression profiling, MESH: Oligonucleotide Array Sequence Analysis, business, vigne, MESH: Chromosome Mapping, Biologie végétale, 010606 plant biology & botany
Abstract: Background Whole genome transcriptomics analysis is a very powerful approach because it gives an overview of the activity of genes in certain cells or tissue types. However, biological interpretation of such results can be rather tedious. MapMan is a software tool that displays large datasets (e.g. gene expression data) onto diagrams of metabolic pathways or other processes and thus enables easier interpretation of results. The grapevine (Vitis vinifera) genome sequence has recently become available bringing a new dimension into associated research. Two microarray platforms were designed based on the TIGR Gene Index database and used in several physiological studies. Results To enable easy and effective visualization of those and further experiments, annotation of Vitis vinifera Gene Index (VvGI version 5) to MapMan ontology was set up. Due to specificities of grape physiology, we have created new pictorial representations focusing on three selected pathways: carotenoid pathway, terpenoid pathway and phenylpropanoid pathway, the products of these pathways being important for wine aroma, flavour and colour, as well as plant defence against pathogens. This new tool was validated on Affymetrix microarrays data obtained during berry ripening and it allowed the discovery of new aspects in process regulation. We here also present results on transcriptional profiling of grape plantlets after exposal to the fungal pathogen Eutypa lata using Operon microarrays including visualization of results with MapMan. The data show that the genes induced in infected plants, encode pathogenesis related proteins and enzymes of the flavonoid metabolism, which are well known as being responsive to fungal infection. Conclusion The extension of MapMan ontology to grapevine together with the newly constructed pictorial representations for carotenoid, terpenoid and phenylpropanoid metabolism provide an alternative approach to the analysis of grapevine gene expression experiments performed with Affymetrix or Operon microarrays. MapMan was first validated on an already published dataset and later used to obtain an overview of transcriptional changes in a susceptible grapevine – Eutypa lata interaction at the time of symptoms development, where we showed that the responsive genes belong to families known to be involved in the plant defence towards fungal infection (PR-proteins, enzymes of the phenylpropanoid pathway).
Published: 2009
Full Text: View/download PDF

37. Mutation detection using ENDO1: Application to disease diagnostics in humans and TILLING and Eco-TILLING in plants

Author: Christine Le Signor, Abdelhafid Bendahmane, Michel Caboche, Marion Dalmais, Julien Schmidt, Elodie Piednoir, Mark Sharkey, Karine Triques, Bénédicte Sturbois, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), UMR 0102 - Unité de Recherche Génétique et Ecophysiologie des Légumineuses, Génétique et Ecophysiologie des Légumineuses à Graines (UMRLEG) (UMR 102), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, and University of Massachusetts System (UMASS)
Subjects: 0106 biological sciences, TILLING, [SDV]Life Sciences [q-bio], Mutant, DNA Mutational Analysis, génomique fonctionnelle, Arabidopsis, 01 natural sciences, chemistry.chemical_compound, Endonuclease, Disease, Genetics, Venous Thrombosis, 0303 health sciences, education.field_of_study, Alanine, Deoxyribonucleases, Genome, lcsh:Cytology, Methodology Article, food and beverages, 3. Good health, méthode de détection, [SDE]Environmental Sciences, lcsh:QH426-470, Population, endonucléase, Molecular Sequence Data, Glycine, Viral quasispecies, Biology, Gene Expression Regulation, Enzymologic, 03 medical and health sciences, Humans, lcsh:QH573-671, nucléase, education, Molecular Biology, Gene, 030304 developmental biology, Base Sequence, Arabidopsis Proteins, Peas, Factor V, BIOLOGIE MOLECULAIRE, lcsh:Genetics, enzyme, chemistry, Amino Acid Substitution, Mutagenesis, Mutation, biology.protein, HIV-1, DNA, 010606 plant biology & botany
Abstract: Background Most enzymatic mutation detection methods are based on the cleavage of heteroduplex DNA by a mismatch-specific endonuclease at mismatch sites and the analysis of the digestion product on a DNA sequencer. Important limitations of these methods are the availability of a mismatch-specific endonuclease, their sensitivity in detecting one allele in pool of DNA, the cost of the analysis and the ease by which the technique could be implemented in a standard molecular biology laboratory. Results The co-agroinfiltration of ENDO1 and p19 constructs into N. benthamiana leaves allowed high level of transient expression of a mismatch-specific and sensitive endonuclease, ENDO1 from Arabidopsis thaliana. We demonstrate the broad range of uses of the produced enzyme in detection of mutations. In human, we report the diagnosis of the G1691A mutation in Leiden factor-V gene associated with venous thrombosis and the fingerprinting of HIV-1 quasispecies in patients subjected to antiretroviral treatments. In plants, we report the use of ENDO1 system for detection of mutant alleles of Retinoblastoma-related gene by TILLING in Pisum sativum and discovery of natural sequence variations by Eco-TILLING in Arabidopsis thaliana. Conclusion We introduce a cost-effective tool based on a simplified purification protocol of a mismatch-specific and sensitive endonuclease, ENDO1. Especially, we report the successful applications of ENDO1 in mutation diagnostics in humans, fingerprinting of complex population of viruses, and in TILLING and Eco-TILLING in plants.
Published: 2008
Full Text: View/download PDF

38. Adaptation and Mitigation in Tropical Tree Plantations

Author: Jean-Paul Laclau, Frédéric Gay, Jean-Pierre Bouillet, Jean-Marc Bouvet, Gilles Chaix, André Clément-Demange, Frédéric Do, Daniel Epron, Bénédicte Favreau, Jean-Marc Gion, Yann Nouvellon, Valérie Pujade-Renaud, Philippe Thaler, Daniel Verhaegen, Philippe Vigneron, UL, Admin, E. Torquebiau, Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Ecologie et Ecophysiologie Forestières [devient SILVA en 2018] (EEF), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Centre de Recherche sur la Durabilité et la Productivité des Plantations Industrielles (Dispositif en Partenariat) (CRDPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-UR Génétique Amélioration Diversité, Institut National de la Recherche Agronomique (INRA)-Institut de Recherche pour le Développement (IRD)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), and Torquebiau, E. (ed.)
Subjects: 0106 biological sciences, Ecophysiology, P40 - Météorologie et climatologie, INNOVATION, [SDV]Life Sciences [q-bio], adaptation aux changements climatiques, forêt tropicale, Photosynthesis, 01 natural sciences, 03 medical and health sciences, Nutrient, ARBRE, ADAPTATION, atténuation des effets du changement climatique, ComputingMilieux_MISCELLANEOUS, BOIS TROPICAUX, 030304 developmental biology, Changement climatique, 2. Zero hunger, 0303 health sciences, Carbon dioxide in Earth's atmosphere, Biomass (ecology), AMELIORATION GENETIQUE, Abiotic stress, Agroforestry, ECOPHYSIOLOGIE, 15. Life on land, K10 - Production forestière, PLANTATIONS, [SDV] Life Sciences [q-bio], Climate change mitigation, GENOMIQUE FONCTIONNELLE, CLIMAT, 13. Climate action, CHANGEMENT CLIMATIQUE, Sustainability, Environmental science, 010606 plant biology & botany
Abstract: Tropical tree plantations are rapidly expanding to meet the growing demand for wood and nonwood forest products. Current research-combining ecophysiology, genetics and functional genomics-aims to enhance the climate change mitigation role of these plantations and their adaptation. The positive effect of the increase in atmospheric carbon dioxide concentration on photosynthesis could boost biomass production, but the higher water and nutrient needs will have to be fulfilled to ensure the sustainability of this positive effect. Multispecies plantations benefitting from positive interactions between species could help maintain production in tropical tree plantations against a background of increasing biotic and abiotic stress.

Catalog

Books, media, physical & digital resources

See catalog results

Searchworks

Select search scope, currently: Articles Catalog books, media & more in Jio Institute collections Articles journal articles & other e-resources

Search

Search Constraints

Refine your results

Search Limiters

Topic

Publication Year Range

Language

Journal

Database

Publisher

38 results on '"génomique fonctionnelle"'

Search Results

Catalog

Select search scope, currently: Articles

Catalog

books, media & more in Jio Institute collections

Articles

journal articles & other e-resources